[Scop | Full Entry | Seq (local cached copy) | More Options ]
HEADER HORMONE/GROWTH FACTOR RECEPTOR 23-JUN-99 1QSV TITLE THE VEGF-BINDING DOMAIN OF FLT-1, 20 NMR STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SECOND EXTRACELLULAR IMMUNOGLOBULIN-LIKE DOMAIN; COMPND 5 SYNONYM: FLT-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 OTHER_DETAILS: MODIFIED QIAGEN PQE30 CONTAINING HIS-TAG SOURCE 7 AND GENENASE CLEAVAGE SITE KEYWDS IMMUNOGLOBULIN-LIKE DOMAIN, I-SET, VEGF RECEPTOR EXPDTA NMR, 20 STRUCTURES AUTHOR M.A.STAROVASNIK,H.W.CHRISTINGER,C.WIESMANN,M.A.CHAMPE, AUTHOR 2 A.M.DE VOS,N.J.SKELTON REVDAT 1 10-NOV-99 1QSV 0 JRNL AUTH M.A.STAROVASNIK,H.W.CHRISTINGER,C.WIESMANN, JRNL AUTH 2 M.A.CHAMPE,A.M.DE VOS,N.J.SKELTON JRNL TITL SOLUTION STRUCTURE OF THE VEGF-BINDING DOMAIN OF JRNL TITL 2 FLT-1: COMPARISON OF ITS FREE AND BOUND STATES. JRNL REF J.MOL.BIOL. V. 293 531 1999 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 95.0 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS, INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 2054 NOE-DERIVED DISTANCE RESTRAINTS, 122 DIHEDRAL REMARK 3 RESTRAINTS, AND 44 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1QSV 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 3.100 (2007-03-17) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB009225. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : 150MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM FLT-1(DOMAIN2) U-15N,13C; REMARK 210 PHOSPHATE BUFFERED SALINE, PH REMARK 210 5.7; 50UM EDTA; 100UM NAN3; REMARK 210 50UM DSS; 1MM FLT-1(DOMAIN2) U REMARK 210 -15N; PHOSPHATE BUFFERED REMARK 210 SALINE, PH 5.7; 50UM EDTA; REMARK 210 100UM NAN3; 50UM DSS REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY, HNHA, REMARK 210 HNHB, 3D_15N_SEPARATED_TOCSY REMARK 210 (32 AND 96 MS), 3D_15N_ REMARK 210 SEPARATED_ROESY (40MS) REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : AMX, INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER, VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR 910901, FELIX 97.0, REMARK 210 DGII 95.0, DISCOVER 95.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED REMARK 210 ANNEALING; MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: AN ADDITIONAL SAMPLE THAT WAS 15% 13C LABELED WAS USED REMARK 210 TO OBTAIN STEREOSPECIFIC ASSIGNMENTS OF PROCHIRAL METHYL REMARK 210 GROUPS. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 16 ILE A 142 C - N - CA ANGL. DEV. = 10.4 DEGREES REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 2 MET A 138 132.71 71.08 REMARK 500 3 ILE A 142 121.22 127.95 REMARK 500 3 ASN A 212 -99.00 52.99 REMARK 500 4 MET A 138 137.77 69.36 REMARK 500 5 LEU A 215 128.91 70.63 REMARK 500 6 MET A 138 157.07 69.76 REMARK 500 7 MET A 138 139.05 66.83 REMARK 500 8 ILE A 142 127.25 108.64 REMARK 500 11 ILE A 142 117.43 114.43 REMARK 500 11 ASN A 212 -76.93 64.78 REMARK 500 13 ILE A 142 122.30 119.73 REMARK 500 13 ASN A 212 -85.34 63.45 REMARK 500 16 ILE A 142 120.08 116.60 REMARK 500 19 ILE A 142 128.40 78.36 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FLT RELATED DB: PDB REMARK 900 1.7 A RESOLUTION CRYSTAL STRUCTURE OF THE SECOND REMARK 900 IMMUNOGLOBULIN DOMAIN OF FLT- 1 IN COMPLEX WITH VEGF REMARK 900 RELATED ID: 1QSZ RELATED DB: PDB REMARK 900 1QSZ CONTAINS THE MINIMIZED MEAN STRUCTURE FOR THE ENSEMBLE REMARK 900 OF STRUCTURES IN 1QSV. DBREF 1QSV A 129 229 UNP P17948 VGFR1_HUMAN 129 229 SEQRES 1 A 101 SER ASP THR GLY ARG PRO PHE VAL GLU MET TYR SER GLU SEQRES 2 A 101 ILE PRO GLU ILE ILE HIS MET THR GLU GLY ARG GLU LEU SEQRES 3 A 101 VAL ILE PRO CYS ARG VAL THR SER PRO ASN ILE THR VAL SEQRES 4 A 101 THR LEU LYS LYS PHE PRO LEU ASP THR LEU ILE PRO ASP SEQRES 5 A 101 GLY LYS ARG ILE ILE TRP ASP SER ARG LYS GLY PHE ILE SEQRES 6 A 101 ILE SER ASN ALA THR TYR LYS GLU ILE GLY LEU LEU THR SEQRES 7 A 101 CYS GLU ALA THR VAL ASN GLY HIS LEU TYR LYS THR ASN SEQRES 8 A 101 TYR LEU THR HIS ARG GLN THR ASN THR ILE HELIX 1 1 SER A 162 THR A 166 5 5 HELIX 2 2 THR A 198 ILE A 202 5 5 SHEET 1 A 5 GLU A 144 MET A 148 0 SHEET 2 A 5 LEU A 215 ARG A 224 1 O ASN A 219 N GLU A 144 SHEET 3 A 5 LEU A 204 THR A 210 -1 O LEU A 205 N TYR A 220 SHEET 4 A 5 THR A 168 LYS A 171 -1 N THR A 168 O GLU A 208 SHEET 5 A 5 ASP A 175 THR A 176 -1 N ASP A 175 O LYS A 171 SHEET 1 B 3 LEU A 154 ILE A 156 0 SHEET 2 B 3 GLY A 191 ILE A 194 -1 N PHE A 192 O ILE A 156 SHEET 3 B 3 ILE A 184 ASP A 187 -1 O ILE A 185 N ILE A 193 SSBOND 1 CYS A 158 CYS A 207 CISPEP 1 PHE A 172 PRO A 173 1 0.40 CISPEP 2 PHE A 172 PRO A 173 2 3.28 CISPEP 3 PHE A 172 PRO A 173 3 5.69 CISPEP 4 PHE A 172 PRO A 173 4 3.75 CISPEP 5 PHE A 172 PRO A 173 5 0.91 CISPEP 6 PHE A 172 PRO A 173 6 3.37 CISPEP 7 PHE A 172 PRO A 173 7 1.89 CISPEP 8 PHE A 172 PRO A 173 8 0.34 CISPEP 9 PHE A 172 PRO A 173 9 6.30 CISPEP 10 PHE A 172 PRO A 173 10 2.21 CISPEP 11 PHE A 172 PRO A 173 11 -0.81 CISPEP 12 PHE A 172 PRO A 173 12 0.07 CISPEP 13 PHE A 172 PRO A 173 13 0.56 CISPEP 14 PHE A 172 PRO A 173 14 1.29 CISPEP 15 PHE A 172 PRO A 173 15 -0.39 CISPEP 16 PHE A 172 PRO A 173 16 0.71 CISPEP 17 PHE A 172 PRO A 173 17 0.77 CISPEP 18 PHE A 172 PRO A 173 18 1.52 CISPEP 19 PHE A 172 PRO A 173 19 0.26 CISPEP 20 PHE A 172 PRO A 173 20 0.71 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1