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HEADER HYDROLASE INHIBITOR 24-NOV-99 1DGN TITLE SOLUTION STRUCTURE OF ICEBERG, AN INHIBITOR OF INTERLEUKIN- TITLE 2 1BETA GENERATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ICEBERG (PROTEASE INHIBITOR); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-90; COMPND 5 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 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ANTIPARALLEL SIX-HELIX BUNDLE, GREEK-KEY EXPDTA NMR, 20 STRUCTURES AUTHOR E.W.HUMKE,S.K.SHRIVER,M.A.STAROVASNIK,W.J.FAIRBROTHER, AUTHOR 2 V.M.DIXIT REVDAT 1 09-OCT-00 1DGN 0 JRNL AUTH E.W.HUMKE,S.K.SHRIVER,M.A.STAROVASNIK, JRNL AUTH 2 W.J.FAIRBROTHER,V.M.DIXIT JRNL TITL ICEBERG: A NOVEL INHIBITOR OF INTERLEUKIN-1BETA JRNL TITL 2 GENERATION. JRNL REF CELL V. 103 99 2000 JRNL REFN ASTM CELLB5 US ISSN 0092-8674 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.1 REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1050 NON-REDUNDANT NOE-DERIVED REMARK 3 DISTANCE RESTRAINTS 88 HYDROGEN-BOND RESTRAINTS 100 DIHEDRAL REMARK 3 ANGLE RESTRAINTS REMARK 4 REMARK 4 1DGN 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 (2007-03-16) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB010070. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 303; 303 REMARK 210 PH : 3.8; 3.8; 3.8 REMARK 210 IONIC STRENGTH : 50 MM SODIUM ACETATE; 50 MM REMARK 210 SODIUM ACETATE; 50 MM SODIUM REMARK 210 ACETATE REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM ICEBERG U-15N; 50MM REMARK 210 SODIUM ACETATE-D3; 20 MM DTT- REMARK 210 D10; 1MM SODIUM AZIDE 2MM REMARK 210 ICEBERG U-15N,13C; 50MM SODIUM REMARK 210 ACETATE-D3; 20MM DTT-D10; 1MM REMARK 210 SODIUM AZIDE 2MM ICEBERG 15%- REMARK 210 13C; 50MM SODIUM ACETATE-D3; REMARK 210 20MM DTT-D10; 1MM SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, HNHA, REMARK 210 HNHB, 3D_15N-SEPARATED_ROESY, REMARK 210 3D_15N-SEPARATED_TOCSY, 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.1, FELIX 97.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 REMARK 210 REMARK 210 REMARK: NULL 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 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 1 LEU A 26 CB LEU A 26 CG 0.031 REMARK 500 2 LEU A 5 CB LEU A 5 CG 0.033 REMARK 500 2 LEU A 26 CB LEU A 26 CG 0.030 REMARK 500 3 ARG A 10 CB ARG A 10 CG 0.030 REMARK 500 3 LEU A 26 CB LEU A 26 CG 0.034 REMARK 500 3 LYS A 67 CB LYS A 67 CG 0.030 REMARK 500 4 ARG A 10 CB ARG A 10 CG 0.033 REMARK 500 4 LEU A 26 CB LEU A 26 CG 0.029 REMARK 500 4 LEU A 89 CG LEU A 89 CD2 0.028 REMARK 500 5 LEU A 5 CB LEU A 5 CG 0.029 REMARK 500 5 LEU A 26 CB LEU A 26 CG 0.028 REMARK 500 5 LEU A 89 CG LEU A 89 CD2 0.028 REMARK 500 6 LEU A 5 CB LEU A 5 CG 0.027 REMARK 500 6 ARG A 10 CB ARG A 10 CG 0.033 REMARK 500 6 LYS A 64 CG LYS A 64 CD 0.036 REMARK 500 7 LEU A 5 CB LEU A 5 CG 0.030 REMARK 500 7 LEU A 26 CB LEU A 26 CG 0.028 REMARK 500 7 LYS A 42 CG LYS A 42 CD 0.043 REMARK 500 7 LYS A 64 CG LYS A 64 CD 0.036 REMARK 500 7 LEU A 89 CG LEU A 89 CD2 0.043 REMARK 500 8 LEU A 5 CB LEU A 5 CG 0.034 REMARK 500 8 ARG A 10 CB ARG A 10 CG 0.033 REMARK 500 8 LEU A 26 CB LEU A 26 CG 0.028 REMARK 500 8 LYS A 42 CG LYS A 42 CD 0.039 REMARK 500 8 LYS A 42 CD LYS A 42 CE 0.033 REMARK 500 10 LEU A 5 CB LEU A 5 CG 0.029 REMARK 500 10 ARG A 10 CB ARG A 10 CG 0.032 REMARK 500 10 LEU A 26 CB LEU A 26 CG 0.031 REMARK 500 10 LEU A 89 CG LEU A 89 CD2 0.044 REMARK 500 11 LEU A 5 CB LEU A 5 CG 0.033 REMARK 500 11 LEU A 26 CB LEU A 26 CG 0.031 REMARK 500 11 LEU A 89 CG LEU A 89 CD2 0.040 REMARK 500 12 LEU A 5 CB LEU A 5 CG 0.036 REMARK 500 12 LEU A 26 CB LEU A 26 CG 0.029 REMARK 500 13 LEU A 5 CB LEU A 5 CG 0.032 REMARK 500 14 LEU A 5 CB LEU A 5 CG 0.031 REMARK 500 14 LYS A 42 CG LYS A 42 CD 0.043 REMARK 500 15 LEU A 5 CB LEU A 5 CG 0.033 REMARK 500 15 LYS A 8 CB LYS A 8 CG 0.034 REMARK 500 15 LEU A 26 CB LEU A 26 CG 0.029 REMARK 500 15 LEU A 60 CB LEU A 60 CG 0.028 REMARK 500 15 LYS A 64 CB LYS A 64 CG 0.028 REMARK 500 16 LEU A 5 CB LEU A 5 CG 0.036 REMARK 500 16 LEU A 26 CB LEU A 26 CG 0.030 REMARK 500 16 GLU A 79 N GLU A 79 CA 0.031 REMARK 500 17 LEU A 5 CB LEU A 5 CG 0.028 REMARK 500 17 LYS A 42 CB LYS A 42 CG 0.032 REMARK 500 18 LEU A 5 CB LEU A 5 CG 0.031 REMARK 500 18 LEU A 26 CB LEU A 26 CG 0.028 REMARK 500 19 LEU A 5 CB LEU A 5 CG 0.035 REMARK 500 19 ARG A 10 CB ARG A 10 CG 0.030 REMARK 500 19 LEU A 26 CB LEU A 26 CG 0.030 REMARK 500 20 LEU A 5 CB LEU A 5 CG 0.030 REMARK 500 20 LEU A 26 CB LEU A 26 CG 0.027 REMARK 500 20 LYS A 42 CB LYS A 42 CG 0.035 REMARK 500 20 LEU A 89 CG LEU A 89 CD2 0.029 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 1 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 ASP A 80 CA - C - N ANGL. DEV. = 3.3 DEGREES REMARK 500 1 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 4 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 4 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 4 ASP A 80 CA - C - N ANGL. DEV. = 3.0 DEGREES REMARK 500 4 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 5 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 5 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 5 ASP A 80 CA - C - N ANGL. DEV. = 3.3 DEGREES REMARK 500 5 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 ASP A 80 CA - C - N ANGL. DEV. = 3.4 DEGREES REMARK 500 6 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 7 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 8 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 8 LYS A 42 CG - CD - CE ANGL. DEV. = 3.4 DEGREES REMARK 500 8 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 8 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 9 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 9 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 9 ASP A 80 CA - C - N ANGL. DEV. = 3.1 DEGREES REMARK 500 9 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 12 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 12 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 12 ASP A 80 CA - C - N ANGL. DEV. = 3.3 DEGREES REMARK 500 12 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 13 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 13 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 13 ASP A 80 CA - C - N ANGL. DEV. = 3.0 DEGREES REMARK 500 13 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.3 DEGREES REMARK 500 14 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 GLY A 65 CA - C - N ANGL. DEV. = 3.7 DEGREES REMARK 500 14 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 15 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 15 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 15 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 16 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 16 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 16 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 17 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 17 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 17 ASP A 80 CA - C - N ANGL. DEV. = 3.0 DEGREES REMARK 500 17 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 18 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 18 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 18 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 19 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 19 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 19 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 20 HIS A 15 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 20 HIS A 75 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES REMARK 500 20 HIS A 90 CE1 - NE2 - CD2 ANGL. DEV. = -3.2 DEGREES DBREF 1DGN A 2 90 UNP P57730 ICBR_HUMAN 2 90 SEQRES 1 A 89 ALA ASP GLN LEU LEU ARG LYS LYS ARG ARG ILE PHE ILE SEQRES 2 A 89 HIS SER VAL GLY ALA GLY THR ILE ASN ALA LEU LEU ASP SEQRES 3 A 89 CYS LEU LEU GLU ASP GLU VAL ILE SER GLN GLU ASP MET SEQRES 4 A 89 ASN LYS VAL ARG ASP GLU ASN ASP THR VAL MET ASP LYS SEQRES 5 A 89 ALA ARG VAL LEU ILE ASP LEU VAL THR GLY LYS GLY PRO SEQRES 6 A 89 LYS SER CYS CYS LYS PHE ILE LYS HIS LEU CYS GLU GLU SEQRES 7 A 89 ASP PRO GLN LEU ALA SER LYS MET GLY LEU HIS HELIX 1 1 GLN A 4 LYS A 9 1 6 HELIX 2 2 LYS A 9 HIS A 15 1 7 HELIX 3 3 GLY A 18 GLU A 33 1 16 HELIX 4 4 SER A 36 ASP A 45 1 10 HELIX 5 5 THR A 49 LYS A 64 1 16 HELIX 6 6 GLY A 65 ASP A 80 1 16 HELIX 7 7 GLN A 82 GLY A 88 5 7 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