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HEADER SERINE PROTEASE 01-FEB-01 1H8D
TITLE X-RAY STRUCTURE OF THE HUMAN ALPHA-THROMBIN COMPLEX WITH A
TITLE 2 TRIPEPTIDE PHOSPHONATE INHIBITOR.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THROMBIN;
COMPND 3 CHAIN: L;
COMPND 4 FRAGMENT: THROMBIN LIGHT CHAIN;
COMPND 5 SYNONYM: COAGULATION FACTOR II;
COMPND 6 EC: 3.4.21.5;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: THROMBIN;
COMPND 9 CHAIN: H;
COMPND 10 FRAGMENT: THROMBIN HEAVY CHAIN;
COMPND 11 SYNONYM: COAGULATION FACTOR II;
COMPND 12 EC: 3.4.21.5;
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: HIRUDIN I;
COMPND 15 CHAIN: I;
COMPND 16 FRAGMENT: RESIDUES 55 TO 64;
COMPND 17 SYNONYM: LEPIRUDIN
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 MOL_ID: 2;
SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 6 ORGANISM_COMMON: HUMAN;
SOURCE 7 MOL_ID: 3;
SOURCE 8 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS;
SOURCE 9 ORGANISM_COMMON: MEDICINAL LEECH
KEYWDS SERINE PROTEASE
EXPDTA X-RAY DIFFRACTION
AUTHOR E.SKORDALAKES,G.G.DODSON,D.GREEN,J.DEADMAN
REVDAT 2 16-AUG-01 1H8D 1 REVDAT JRNL REMARK SSBOND
REVDAT 2 2 1 LINK HETATM CONECT MASTER
REVDAT 1 26-FEB-01 1H8D 0
JRNL AUTH E.SKORDALAKES,G.G.DODSON,D.S.GREEN,C.A.GOODWIN,
JRNL AUTH 2 M.F.SCULLY,H.R.HUDSON,V.V.KAKKAR,J.J.DEADMAN
JRNL TITL INHIBITION OF HUMAN ALPHA-THROMBIN BY A
JRNL TITL 2 PHOSPHONATE TRIPEPTIDE PROCEEDS VIA A METASTABLE
JRNL TITL 3 PENTACOORDINATED PHOSPHORUS INTERMEDIATE.
JRNL REF J.MOL.BIOL. V. 311 549 2001
JRNL REFN ASTM JMOBAK UK ISSN 0022-2836
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.A.BERTRAND,J.OLEKSYSZYN,C.M.KAM,B.BODUSZEK,
REMARK 1 AUTH 2 S.PRESNELL,R.R.PLASKON,F.L.SUDDATH,J.C.POWERS,
REMARK 1 AUTH 3 L.D.WILLIAMS
REMARK 1 TITL INHIBITION OF TRYPSIN AND THROMBIN BY AMINO
REMARK 1 TITL 2 (4-AMIDINOPHENYL)METHANEPHOSPHONATE DIPHENYL ESTER
REMARK 1 TITL 3 DERIVATIVES: X-RAY AND MOLECULAR MODELS
REMARK 1 REF BIOCHEMISTRY V. 35 3147 1996
REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. 1.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4
REMARK 3 NUMBER OF REFLECTIONS : 68615
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.170
REMARK 3 FREE R VALUE : 0.220
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2346
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 57
REMARK 3 SOLVENT ATOMS : NULL
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 16.27
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): NULL
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.008 ; NULL
REMARK 3 ANGLE DISTANCE (A) : 1.200 ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1H8D COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 4
REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY.
REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-31)
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI.
REMARK 100 THE EBI ID CODE IS EBI-5851.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-JUN-1998
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.20
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SRS
REMARK 200 BEAMLINE : PX7.2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.48800
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68615
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400
REMARK 200 RESOLUTION RANGE LOW (A) : 15.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4
REMARK 200 DATA REDUNDANCY : 3.000
REMARK 200 R MERGE (I) : 0.05200
REMARK 200 R SYM (I) : 0.05600
REMARK 200 FOR THE DATA SET : 23.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6
REMARK 200 DATA REDUNDANCY IN SHELL : 2.00
REMARK 200 R MERGE FOR SHELL (I) : 0.14200
REMARK 200 R SYM FOR SHELL (I) : 0.13100
REMARK 200 FOR SHELL : 6.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMEN
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: 1HGT
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.2
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 1/2+X,1/2+Y,Z
REMARK 290 4555 1/2-X,1/2+Y,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.32000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.80000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.32000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.80000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I, K, O, P, R, S
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH S 55 LIES ON A SPECIAL POSITION.
REMARK 375 HOH S 57 LIES ON A SPECIAL POSITION.
REMARK 375 HOH S 258 LIES ON A SPECIAL POSITION.
REMARK 375 HOH S 269 LIES ON A SPECIAL POSITION.
REMARK 375 HOH S 531 LIES ON A SPECIAL POSITION.
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU L 1A CG CD OE1 OE2
REMARK 470 ASP L 1C OD1 OD2
REMARK 470 CYS L 1 N
REMARK 470 SER L 14L N CA C O CB
REMARK 470 ARG H 75 CD NE CZ NH1 NH2
REMARK 470 LYS H 236 CD CE NZ
REMARK 470 CYS H 259 N CA C O CB
REMARK 470 SER H 261 N CA C O CB
REMARK 470 SER H 262 N CA C O CB
REMARK 470 VAL H 263 N CA C O CB CG1
REMARK 470 LEU H 264 N CA C O CB CG CD1
REMARK 470 ILE H 265 N CA C O CB CG1 CG2
REMARK 470 VAL H 266 N CA C O CB CG1
REMARK 470 VAL H 267 N CA C O CB CG1
REMARK 470 CYS H 268 N CA C O CB
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI
REMARK 500 CG1 ILE H 90 CD1 ILE H 265 0.71
REMARK 500 CG LEU H 85 CD2 LEU H 264 0.80
REMARK 500 CD1 ILE H 90 CD1 ILE H 265 1.16
REMARK 500 NZ LYS L 9 O HOH O 42 1.24
REMARK 500 CB SER L 11 OG SER L 14L 1.48
REMARK 500 CB SER H 27 OG SER H 261 1.48
REMARK 500 CB VAL H 66 CG2 VAL H 263 1.48
REMARK 500 CB SER H 72 OG SER H 262 1.49
REMARK 500 CB VAL H 138 CG2 VAL H 266 1.49
REMARK 500 CB VAL H 157 CG2 VAL H 267 1.49
REMARK 500 CB LEU H 85 CD2 LEU H 264 1.50
REMARK 500 CB ILE H 90 CD1 ILE H 265 1.50
REMARK 500 O ILE L 14K O HOH O 66 1.54
REMARK 500 CD1 LEU H 85 CD2 LEU H 264 1.72
REMARK 500 CB CYS H 42 SG CYS H 259 1.73
REMARK 500 SD MET H 180 O HOH S 324 1.75
REMARK 500 C54 PHW K 1 O HOH S 504 1.79
REMARK 500 C52 PHW K 1 O HOH P 6 1.80
REMARK 500 O HOH O 45 O HOH O 47 1.82
REMARK 500 O HOH S 30 O HOH S 109 1.83
REMARK 500 OE1 GLU L 13 O HOH O 54 1.88
REMARK 500 O HOH O 24 O HOH O 43 1.88
REMARK 500 O HOH R 31 O HOH R 32 1.88
REMARK 500 SD MET H 84 O HOH R 38 1.94
REMARK 500 CG1 VAL H 66 CG2 VAL H 263 1.97
REMARK 500 O HOH O 11 O HOH O 12 1.97
REMARK 500 O HOH S 231 O HOH S 503 1.99
REMARK 500 O HOH S 1 O HOH S 27 2.00
REMARK 500 O HOH S 37 O HOH S 142 2.00
REMARK 500 N THR H 177 CE MET H 180 2.01
REMARK 500 O HOH S 152 O HOH S 153 2.02
REMARK 500 O HOH S 203 O HOH S 220 2.02
REMARK 500 NZ LYS H 87 O HOH S 290 2.03
REMARK 500 O HOH S 12 O HOH S 83 2.04
REMARK 500 O HOH S 28 O HOH S 103 2.04
REMARK 500 CG LYS H 236 O HOH S 67 2.05
REMARK 500 O LEU I 10 O HOH R 39 2.05
REMARK 500 O ILE L 14K O HOH O 59 2.06
REMARK 500 O HOH S 25 O HOH S 301 2.06
REMARK 500 O HOH S 140 O HOH S 157 2.06
REMARK 500 O HOH S 482 O HOH S 483 2.06
REMARK 500 O HOH S 16 O HOH S 169 2.08
REMARK 500 O HOH S 247 O HOH S 550 2.08
REMARK 500 CG ARG H 50 O HOH S 185 2.09
REMARK 500 NE ARG H 97 O HOH S 317 2.09
REMARK 500 OE1 GLN H 151 O HOH S 396 2.09
REMARK 500 CG GLU I 4 O HOH R 28 2.09
REMARK 500 C53 PHW K 1 O HOH P 6 2.09
REMARK 500 O HOH S 243 O HOH S 539 2.09
REMARK 500 O HOH S 89 O HOH S 329 2.10
REMARK 500 O HOH S 369 O HOH S 406 2.10
REMARK 500 O HOH S 126 O HOH S 347 2.11
REMARK 500 OE2 GLU H 127 O HOH S 364 2.12
REMARK 500 O HOH S 135 O HOH S 365 2.12
REMARK 500 O HOH S 326 O HOH S 329 2.12
REMARK 500 O HOH O 23 O HOH S 122 2.13
REMARK 500 O HOH O 34 O HOH S 404 2.13
REMARK 500 O HOH S 57 O HOH S 277 2.13
REMARK 500 O HOH S 138 O HOH S 227 2.13
REMARK 500 O HOH S 194 O HOH S 456 2.13
REMARK 500 O HOH S 60 O HOH S 125 2.14
REMARK 500 O HOH S 89 O HOH S 304 2.14
REMARK 500 CE LYS H 87 O HOH S 290 2.15
REMARK 500 OE1 GLN H 244 O HOH S 551 2.15
REMARK 500 O HOH R 14 O HOH R 15 2.15
REMARK 500 O HOH S 41 O HOH S 381 2.15
REMARK 500 O HOH S 363 O HOH S 365 2.15
REMARK 500 OG SER L 11 OG SER L 14L 2.16
REMARK 500 CD ARG H 165 O HOH S 415 2.16
REMARK 500 OD1 ASP H 243 O HOH S 548 2.16
REMARK 500 O HOH S 183 O HOH S 184 2.16
REMARK 500 O HOH S 193 O HOH S 459 2.17
REMARK 500 O HOH S 260 O HOH S 264 2.17
REMARK 500 O HOH S 411 O HOH S 438 2.17
REMARK 500 O HOH S 214 O HOH S 222 2.18
REMARK 500 O HOH S 365 O HOH S 367 2.18
REMARK 500 C ILE L 14K O HOH O 59 2.19
REMARK 500 O HOH O 56 O HOH O 65 2.19
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH S 459 O HOH S 459 2556 1.46
REMARK 500 O HOH S 207 O HOH S 347 3545 1.84
REMARK 500 O HOH O 15 O HOH S 14 3455 1.85
REMARK 500 O HOH S 56 O HOH S 56 2555 2.01
REMARK 500 O HOH S 4 O HOH S 169 2656 2.04
REMARK 500 O HOH O 25 O HOH S 220 3455 2.12
REMARK 500 O HOH S 363 O HOH S 520 4556 2.17
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 CYS L 1 CA CYS L 1 CB 0.547
REMARK 500 CYS L 1 CA CYS L 1 C 1.155
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 CYS L 1 CB - CA - C ANGL. DEV. =-49.2 DEGREES
REMARK 500 CYS L 1 CA - CB - SG ANGL. DEV. = 22.1 DEGREES
REMARK 500 CYS H 42 CA - CB - SG ANGL. DEV. = 18.0 DEGREES
REMARK 525
REMARK 525 SOLVENT
REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED
REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE
REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL
REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH S 2 DISTANCE = 6.70 ANGSTROMS
REMARK 525 HOH S 4 DISTANCE = 10.43 ANGSTROMS
REMARK 525 HOH R 20 DISTANCE = 5.35 ANGSTROMS
REMARK 525 HOH S 28 DISTANCE = 6.08 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 SITE_DESCRIPTION: TRIPEPTIDE PHOSPHONATE INHIBITOR BINDING
DBREF 1H8D L 1 14L UNP P00734 THRB_HUMAN 333 361
DBREF 1H8D H 16 259 UNP P00734 THRB_HUMAN 364 622
DBREF 1H8D I 1 10 UNP P01050 ITH1_HIRME 55 64
SEQADV 1H8D TYS I 9 UNP P01050 TYR 63 MODIFIED RESIDUE
SEQRES 1 L 29 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS
SEQRES 2 L 29 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER
SEQRES 3 L 29 TYR ILE SER
SEQRES 1 H 260 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO
SEQRES 2 H 260 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU
SEQRES 3 H 260 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU
SEQRES 4 H 260 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS
SEQRES 5 H 260 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS
SEQRES 6 H 260 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE
SEQRES 7 H 260 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN
SEQRES 8 H 260 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS
SEQRES 9 H 260 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO
SEQRES 10 H 260 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU
SEQRES 11 H 260 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN
SEQRES 12 H 260 LEU LYS GLU THR GLY GLN PRO SER VAL LEU GLN VAL VAL
SEQRES 13 H 260 ASN LEU PRO ILE VAL GLU ARG PRO VAL CYS LYS ASP SER
SEQRES 14 H 260 THR ARG ILE ARG ILE THR ASP ASN MET PHE CYS ALA GLY
SEQRES 15 H 260 TYR LYS PRO ASP GLU GLY LYS ARG GLY ASP ALA CYS GLU
SEQRES 16 H 260 GLY ASP SER GLY GLY PRO PHE VAL MET LYS SER PRO PHE
SEQRES 17 H 260 ASN ASN ARG TRP TYR GLN MET GLY ILE VAL SER TRP GLY
SEQRES 18 H 260 GLU GLY CYS ASP ARG ASP GLY LYS TYR GLY PHE TYR THR
SEQRES 19 H 260 HIS VAL PHE ARG LEU LYS LYS TRP ILE GLN LYS VAL ILE
SEQRES 20 H 260 ASP GLN PHE GLY CYS SER SER VAL LEU ILE VAL VAL CYS
SEQRES 1 I 10 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU
MODRES 1H8D TYS I 9 TYR SULFONATED TYROSINE
HET TYS I 9 16
HET PHW K 1 53
HETNAM TYS SULFONATED TYROSINE
HETNAM PHW BETA-PHENYL-N-{[(PHENYLMETHYL)OXY]CARBONYL}-D-
HETNAM 2 PHW PHENYLALANYL-N- [(1S,3E)-1-[DIHYDROXY(METHYLOXY)
HETNAM 3 PHW (PHENYLOXY)-LAMBDA5-PHOSPHANYL]-4- (METHYLOXY)BUT-3-
HETNAM 4 PHW ENYL]-D-PROLINAMIDE
HETSYN PHW PHENYLMETHYL (1R)-2-[(2R)-2-({[(1S,3E)-1-
HETSYN 2 PHW [DIHYDROXY(METHYLOXY)(PHENYLOXY)- LAMBDA5-PHOSPHANYL]-
HETSYN 3 PHW 4-(METHYLOXY)BUT-3-ENYL]AMINO}CARBONYL)PYRROLIDIN-1-
HETSYN 4 PHW YL]- 1-(DIPHENYLMETHYL)-2-OXOETHYLCARBAMATE
FORMUL 3 TYS C9 H11 N O6 S
FORMUL 4 PHW C40 H46 N3 O9 P
FORMUL 5 HOH *684(H2 O)
HELIX 1 9 PHE L 7 SER L 11 5 5
HELIX 2 10 THR L 14B TYR L 14J 1 9
HELIX 3 1 ALA H 55 CYS H 58 5 4
HELIX 4 2 PRO H 60B ASP H 60E 5 4
HELIX 5 3 THR H 60I ASN H 62 5 3
HELIX 6 4 ASP H 125 LEU H 130 1 9
HELIX 7 5 GLU H 164 SER H 171 1 8
HELIX 8 6 LYS H 185 GLY H 186C 5 5
HELIX 9 7 LEU H 234 GLY H 246 1 13
HELIX 10 8 PRO I 6 LEU I 10 5 5
SHEET 1 HA 7 SER H 20 ASP H 21 0
SHEET 2 HA 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20
SHEET 3 HA 7 LYS H 135 GLY H 140 -1 O GLY H 136 N LEU H 160
SHEET 4 HA 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139
SHEET 5 HA 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201
SHEET 6 HA 7 GLY H 226 HIS H 230 -1 O PHE H 227 N SER H 214
SHEET 7 HA 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228
SHEET 1 HB 7 LYS H 81 SER H 83 0
SHEET 2 HB 7 LEU H 64 ILE H 68 -1 O VAL H 66 N SER H 83
SHEET 3 HB 7 GLN H 30 ARG H 35 0
SHEET 4 HB 7 GLU H 39 LEU H 46 0
SHEET 5 HB 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45
SHEET 6 HB 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54
SHEET 7 HB 7 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107
SHEET 1 HC 2 LEU H 60 TYR H 60A 0
SHEET 2 HC 2 LYS H 60F ASN H 60G 0
SSBOND 1 CYS H 42 CYS H 58
SSBOND 2 CYS H 122 CYS L 1
SSBOND 3 CYS H 168 CYS H 182
SSBOND 4 CYS H 191 CYS H 220
LINK C GLU I 8 N TYS I 9
LINK C TYS I 9 N LEU I 10
CISPEP 1 SER H 36A PRO H 37 0 -0.79
SITE 1 AC1 23 HIS H 57 TRP H 60D TYR H 60A GLU H 97A
SITE 2 AC1 23 GLU H 146 ALA H 190 CYS H 191 GLU H 192
SITE 3 AC1 23 SER H 195 TRP H 215 GLY H 216 GLU H 217
SITE 4 AC1 23 GLY H 219 CYS H 220 HOH P 1 HOH P 2
SITE 5 AC1 23 HOH P 3 HOH P 4 HOH P 5 HOH P 6
SITE 6 AC1 23 HOH P 7 HOH S 517 HOH S 545
CRYST1 70.640 71.600 71.900 90.00 100.35 90.00 C 1 2 1 5
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.014156 0.000000 0.002585 0.00000
SCALE2 0.000000 0.013966 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014138 0.00000