HEADER SIGNALING PROTEIN 03-MAR-20 5R8H TITLE PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGMENT TITLE 2 Z111716368 IN COMPLEX WITH INTERLEUKIN-1 BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-1 BETA,CATABOLIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IL1B, IL1F2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IL-1 BETA, SIGNALING PROTEIN, SGC - DIAMOND I04-1 FRAGMENT SCREENING, KEYWDS 2 PANDDA, XCHEMEXPLORER EXPDTA X-RAY DIFFRACTION AUTHOR G.F.DE NICOLA,C.E.NICHOLS REVDAT 4 06-MAR-24 5R8H 1 REMARK REVDAT 3 05-AUG-20 5R8H 1 JRNL REVDAT 2 22-JUL-20 5R8H 1 JRNL REVDAT 1 22-APR-20 5R8H 0 JRNL AUTH C.NICHOLS,J.NG,A.KESHU,G.KELLY,M.R.CONTE,M.S.MARBER, JRNL AUTH 2 F.FRATERNALI,G.F.DE NICOLA JRNL TITL MINING THE PDB FOR TRACTABLE CASES WHERE X-RAY JRNL TITL 2 CRYSTALLOGRAPHY COMBINED WITH FRAGMENT SCREENS CAN BE USED JRNL TITL 3 TO SYSTEMATICALLY DESIGN PROTEIN-PROTEIN INHIBITORS: TWO JRNL TITL 4 TEST CASES ILLUSTRATED BY IL1 BETA-IL1R AND P38 ALPHA-TAB1 JRNL TITL 5 COMPLEXES. JRNL REF J.MED.CHEM. V. 63 7559 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32543856 JRNL DOI 10.1021/ACS.JMEDCHEM.0C00403 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 33652 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1776 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2450 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3590 REMARK 3 BIN FREE R VALUE SET COUNT : 141 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1190 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.838 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2251 ; 0.022 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1665 ; 0.003 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2492 ; 2.654 ; 1.668 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3921 ; 1.571 ; 1.598 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 256 ; 8.094 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;31.417 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 332 ;14.997 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;15.443 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 226 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2287 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 363 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1199 ; 3.567 ; 3.130 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1140 ; 3.645 ; 3.012 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1222 ; 5.128 ; 4.415 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5R8H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1001402902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.96871 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.71800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 2NVH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M AMMONIUM SULPHATE, 0.1M TRIS REMARK 280 PH7.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 37.73500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.60250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.86750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 153 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 ALA A 1 CB REMARK 470 GLN A 34 CG CD OE1 NE2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 LYS A 55 CD CE NZ REMARK 470 LYS A 93 CE NZ REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 GLN A 141 CG CD OE1 NE2 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 DISTANCE REMARK 500 O HOH A 384 O HOH A 385 1.53 REMARK 500 REMARK 500 REMARK: NULL 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 A 316 O HOH A 340 3644 1.94 REMARK 500 O HOH A 346 O HOH A 384 3654 2.04 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 13 CB SER A 13 OG -0.090 REMARK 500 MET A 36 CB MET A 36 CG 0.234 REMARK 500 GLU A 83 CD GLU A 83 OE1 -0.074 REMARK 500 GLU A 111 CG GLU A 111 CD 0.094 REMARK 500 GLU A 111 CD GLU A 111 OE1 -0.111 REMARK 500 GLU A 128 CD GLU A 128 OE2 -0.067 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL A 40 CA - CB - CG2 ANGL. DEV. = 11.9 DEGREES REMARK 500 PHE A 46 CB - CG - CD1 ANGL. DEV. = 4.6 DEGREES REMARK 500 PRO A 78 N - CA - CB ANGL. DEV. = 8.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 75 53.02 27.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 127 -10.83 REMARK 500 PHE A 150 11.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 T91 A 203 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T91 A 203 DBREF 5R8H A 1 153 UNP P01584 IL1B_HUMAN 117 269 SEQRES 1 A 153 ALA PRO VAL ARG SER LEU ASN CYS THR LEU ARG ASP SER SEQRES 2 A 153 GLN GLN LYS SER LEU VAL MET SER GLY PRO TYR GLU LEU SEQRES 3 A 153 LYS ALA LEU HIS LEU GLN GLY GLN ASP MET GLU GLN GLN SEQRES 4 A 153 VAL VAL PHE SER MET SER PHE VAL GLN GLY GLU GLU SER SEQRES 5 A 153 ASN ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLU LYS SEQRES 6 A 153 ASN LEU TYR LEU SER CYS VAL LEU LYS ASP ASP LYS PRO SEQRES 7 A 153 THR LEU GLN LEU GLU SER VAL ASP PRO LYS ASN TYR PRO SEQRES 8 A 153 LYS LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS ILE SEQRES 9 A 153 GLU ILE ASN ASN LYS LEU GLU PHE GLU SER ALA GLN PHE SEQRES 10 A 153 PRO ASN TRP TYR ILE SER THR SER GLN ALA GLU ASN MET SEQRES 11 A 153 PRO VAL PHE LEU GLY GLY THR LYS GLY GLY GLN ASP ILE SEQRES 12 A 153 THR ASP PHE THR MET GLN PHE VAL SER SER HET SO4 A 201 5 HET SO4 A 202 5 HET T91 A 203 11 HETNAM SO4 SULFATE ION HETNAM T91 N-[2-(1H-BENZIMIDAZOL-2-YL)ETHYL]-2,2- HETNAM 2 T91 DIMETHYLPROPANAMIDE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 T91 C14 H19 N3 O FORMUL 5 HOH *113(H2 O) HELIX 1 AA1 GLN A 32 GLN A 39 5 8 HELIX 2 AA2 GLU A 96 ARG A 98 5 3 SHEET 1 AA1 7 ARG A 4 ASP A 12 0 SHEET 2 AA1 7 PHE A 42 PHE A 46 -1 O PHE A 42 N CYS A 8 SHEET 3 AA1 7 LYS A 55 LEU A 62 -1 O GLY A 61 N SER A 43 SHEET 4 AA1 7 VAL A 100 ILE A 106 -1 O PHE A 101 N VAL A 58 SHEET 5 AA1 7 LYS A 109 SER A 114 -1 O GLU A 113 N ASN A 102 SHEET 6 AA1 7 PHE A 146 PHE A 150 -1 O PHE A 146 N LEU A 110 SHEET 7 AA1 7 ARG A 4 ASP A 12 -1 N ARG A 11 O THR A 147 SHEET 1 AA2 3 SER A 17 MET A 20 0 SHEET 2 AA2 3 LEU A 26 LEU A 29 -1 O LYS A 27 N VAL A 19 SHEET 3 AA2 3 MET A 130 PRO A 131 -1 O MET A 130 N ALA A 28 SHEET 1 AA3 2 LEU A 67 LYS A 74 0 SHEET 2 AA3 2 LYS A 77 SER A 84 -1 O LYS A 77 N LYS A 74 SHEET 1 AA4 2 TYR A 121 SER A 123 0 SHEET 2 AA4 2 PHE A 133 GLY A 135 -1 O PHE A 133 N SER A 123 CISPEP 1 TYR A 90 PRO A 91 0 -4.30 SITE 1 AC1 5 ALA A 1 VAL A 3 LYS A 92 LYS A 93 SITE 2 AC1 5 HOH A 309 SITE 1 AC2 3 ARG A 98 HOH A 302 HOH A 328 SITE 1 AC3 5 GLU A 37 GLN A 39 VAL A 41 LYS A 63 SITE 2 AC3 5 HOH A 407 CRYST1 54.610 54.610 75.470 90.00 90.00 90.00 P 43 4 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 0.018312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013250 0.00000 TER 1241 SER A 152 HETATM 1242 S SO4 A 201 29.408 14.054 50.720 1.00108.63 S HETATM 1243 O1 SO4 A 201 28.970 13.228 49.608 1.00138.43 O HETATM 1244 O2 SO4 A 201 29.211 15.484 50.381 1.00 80.66 O HETATM 1245 O3 SO4 A 201 28.625 13.677 51.873 1.00 43.86 O HETATM 1246 O4 SO4 A 201 30.819 13.798 50.960 1.00102.91 O HETATM 1247 S SO4 A 202 23.870 3.600 61.095 1.00 52.38 S HETATM 1248 O1 SO4 A 202 25.296 3.765 60.687 1.00 48.48 O HETATM 1249 O2 SO4 A 202 23.017 3.838 59.939 1.00 54.81 O HETATM 1250 O3 SO4 A 202 23.688 2.290 61.664 1.00 63.85 O HETATM 1251 O4 SO4 A 202 23.439 4.624 62.079 1.00 44.38 O HETATM 1252 N1 T91 A 203 50.954 8.886 63.037 0.40 37.57 N HETATM 1253 C5 T91 A 203 53.055 11.784 62.772 0.40 40.12 C HETATM 1254 C6 T91 A 203 53.034 10.251 63.039 0.40 42.89 C HETATM 1255 C7 T91 A 203 51.915 9.508 62.362 0.40 35.32 C HETATM 1256 C8 T91 A 203 49.974 8.492 62.125 0.40 35.58 C HETATM 1257 C10 T91 A 203 47.881 7.796 61.286 0.40 25.89 C HETATM 1258 C13 T91 A 203 50.420 8.818 60.831 0.40 32.60 C HETATM 1259 C11 T91 A 203 48.371 8.061 59.979 0.40 29.23 C HETATM 1260 C12 T91 A 203 49.627 8.584 59.770 0.40 27.64 C HETATM 1261 C9 T91 A 203 48.682 7.989 62.366 0.40 29.52 C HETATM 1262 N2 T91 A 203 51.709 9.503 61.024 0.40 33.57 N HETATM 1263 O HOH A 301 28.359 -0.507 53.605 1.00 48.77 O HETATM 1264 O HOH A 302 21.618 6.082 61.836 1.00 49.36 O HETATM 1265 O HOH A 303 32.718 7.279 79.451 1.00 39.92 O HETATM 1266 O HOH A 304 21.275 2.201 78.550 1.00 37.83 O HETATM 1267 O HOH A 305 28.755 8.412 51.519 1.00 38.94 O HETATM 1268 O HOH A 306 37.687 22.156 79.397 1.00 48.62 O HETATM 1269 O HOH A 307 40.020 30.859 72.721 1.00 54.94 O HETATM 1270 O HOH A 308 53.319 21.303 56.917 1.00 55.01 O HETATM 1271 O HOH A 309 26.470 13.376 53.272 1.00 35.31 O HETATM 1272 O HOH A 310 26.709 21.856 76.134 1.00 43.27 O HETATM 1273 O HOH A 311 38.085 10.584 57.608 1.00 28.26 O HETATM 1274 O HOH A 312 36.691 1.212 70.950 1.00 31.34 O HETATM 1275 O HOH A 313 27.665 22.665 60.274 1.00 49.77 O HETATM 1276 O HOH A 314 42.128 15.160 55.936 1.00 34.99 O HETATM 1277 O HOH A 315 40.915 9.854 84.966 1.00 45.99 O HETATM 1278 O HOH A 316 46.393 3.927 56.085 1.00 50.64 O HETATM 1279 O HOH A 317 38.376 19.281 83.015 1.00 39.88 O HETATM 1280 O HOH A 318 48.905 14.615 82.658 1.00 29.20 O HETATM 1281 O HOH A 319 50.030 5.168 67.543 1.00 41.45 O HETATM 1282 O HOH A 320 46.978 8.975 79.932 1.00 24.87 O HETATM 1283 O HOH A 321 26.306 20.227 66.421 1.00 30.55 O HETATM 1284 O HOH A 322 50.374 5.511 84.604 1.00 42.36 O HETATM 1285 O HOH A 323 53.633 14.954 73.951 1.00 26.09 O HETATM 1286 O HOH A 324 37.065 12.680 59.104 1.00 28.19 O HETATM 1287 O HOH A 325 37.491 15.207 52.876 1.00 43.19 O HETATM 1288 O HOH A 326 35.868 14.511 81.853 1.00 34.72 O HETATM 1289 O HOH A 327 34.126 11.107 64.615 1.00 19.43 O HETATM 1290 O HOH A 328 22.868 6.423 58.671 1.00 45.40 O HETATM 1291 O HOH A 329 46.868 13.323 67.925 1.00 20.88 O HETATM 1292 O HOH A 330 33.814 -0.113 67.993 1.00 52.81 O HETATM 1293 O HOH A 331 32.800 20.123 54.936 1.00 36.63 O HETATM 1294 O HOH A 332 25.207 6.995 70.091 1.00 30.58 O HETATM 1295 O HOH A 333 49.095 13.669 69.692 1.00 22.90 O HETATM 1296 O HOH A 334 37.160 17.852 75.269 1.00 21.52 O HETATM 1297 O HOH A 335 27.658 22.799 72.634 1.00 40.54 O HETATM 1298 O HOH A 336 35.742 4.267 76.354 1.00 40.61 O HETATM 1299 O HOH A 337 38.172 4.797 77.039 1.00 38.76 O HETATM 1300 O HOH A 338 28.506 12.357 69.526 1.00 25.68 O HETATM 1301 O HOH A 339 41.774 7.104 81.290 1.00 31.62 O HETATM 1302 O HOH A 340 56.966 8.567 76.041 1.00 42.23 O HETATM 1303 O HOH A 341 31.338 21.882 60.444 1.00 28.03 O HETATM 1304 O HOH A 342 43.574 23.920 80.680 1.00 56.01 O HETATM 1305 O HOH A 343 36.000 25.479 67.324 1.00 28.80 O HETATM 1306 O HOH A 344 29.850 1.805 61.365 1.00 43.43 O HETATM 1307 O HOH A 345 48.488 21.322 74.548 1.00 27.89 O HETATM 1308 O HOH A 346 37.344 25.072 62.918 1.00 43.73 O HETATM 1309 O HOH A 347 27.844 32.626 66.946 1.00 48.51 O HETATM 1310 O HOH A 348 39.426 8.576 58.621 1.00 28.52 O HETATM 1311 O HOH A 349 26.902 5.417 54.829 1.00 43.80 O HETATM 1312 O HOH A 350 38.045 5.498 50.855 1.00 36.34 O HETATM 1313 O HOH A 351 26.813 15.370 60.361 1.00 36.75 O HETATM 1314 O HOH A 352 42.079 9.992 55.793 1.00 44.16 O HETATM 1315 O HOH A 353 39.352 11.880 55.526 1.00 36.73 O HETATM 1316 O HOH A 354 51.892 17.309 64.920 1.00 33.16 O HETATM 1317 O HOH A 355 33.273 29.349 73.736 1.00 57.08 O HETATM 1318 O HOH A 356 24.257 22.157 78.615 1.00 35.61 O HETATM 1319 O HOH A 357 24.555 14.017 62.994 1.00 33.41 O HETATM 1320 O HOH A 358 53.456 17.071 66.850 1.00 44.35 O HETATM 1321 O HOH A 359 28.682 0.732 68.437 1.00 47.59 O HETATM 1322 O HOH A 360 44.308 9.492 79.438 1.00 24.76 O HETATM 1323 O HOH A 361 45.877 20.634 58.181 1.00 40.53 O HETATM 1324 O HOH A 362 51.467 8.227 85.411 1.00 38.77 O HETATM 1325 O HOH A 363 31.650 -1.091 62.883 1.00 47.82 O HETATM 1326 O HOH A 364 39.299 11.219 87.864 1.00 56.12 O HETATM 1327 O HOH A 365 33.823 -1.113 64.841 1.00 31.97 O HETATM 1328 O HOH A 366 45.344 18.266 55.602 1.00 38.70 O HETATM 1329 O HOH A 367 25.117 19.996 68.921 1.00 36.24 O HETATM 1330 O HOH A 368 34.591 6.420 77.453 1.00 26.21 O HETATM 1331 O HOH A 369 25.653 22.170 59.138 1.00 55.65 O HETATM 1332 O HOH A 370 63.398 14.628 73.579 1.00 44.24 O HETATM 1333 O HOH A 371 40.946 20.414 81.341 1.00 31.73 O HETATM 1334 O HOH A 372 44.983 24.859 69.184 1.00 38.70 O HETATM 1335 O HOH A 373 24.139 4.835 71.921 1.00 35.97 O HETATM 1336 O HOH A 374 29.531 2.040 57.346 1.00 30.49 O HETATM 1337 O HOH A 375 22.510 19.626 65.181 1.00 43.71 O HETATM 1338 O HOH A 376 42.923 12.222 86.172 1.00 36.65 O HETATM 1339 O HOH A 377 37.755 8.275 51.733 1.00 39.98 O HETATM 1340 O HOH A 378 24.299 0.097 76.993 1.00 46.91 O HETATM 1341 O HOH A 379 29.589 7.055 48.941 1.00 56.91 O HETATM 1342 O HOH A 380 28.656 3.385 59.661 1.00 35.01 O HETATM 1343 O HOH A 381 28.059 2.870 55.090 1.00 37.13 O HETATM 1344 O HOH A 382 47.159 17.240 52.087 1.00 61.87 O HETATM 1345 O HOH A 383 24.466 7.671 65.446 1.00 27.29 O HETATM 1346 O HOH A 384 24.876 15.489 80.804 1.00 37.27 O HETATM 1347 O HOH A 385 25.072 14.330 81.780 1.00 39.16 O HETATM 1348 O HOH A 386 39.900 5.620 73.184 1.00 29.56 O HETATM 1349 O HOH A 387 36.868 31.901 75.616 1.00 53.49 O HETATM 1350 O HOH A 388 49.793 23.592 69.172 1.00 50.67 O HETATM 1351 O HOH A 389 27.698 2.134 66.822 1.00 46.03 O HETATM 1352 O HOH A 390 48.949 -0.497 69.553 1.00 58.81 O HETATM 1353 O HOH A 391 23.713 26.118 62.516 1.00 49.97 O HETATM 1354 O HOH A 392 38.054 4.031 72.365 1.00 43.37 O HETATM 1355 O HOH A 393 46.886 -0.343 66.777 1.00 53.07 O HETATM 1356 O HOH A 394 45.045 9.679 86.728 1.00 41.44 O HETATM 1357 O HOH A 395 35.707 28.120 66.936 1.00 35.74 O HETATM 1358 O HOH A 396 48.884 23.478 75.843 1.00 36.79 O HETATM 1359 O HOH A 397 52.474 19.407 63.411 1.00 39.66 O HETATM 1360 O HOH A 398 53.120 22.290 54.823 1.00 58.18 O HETATM 1361 O HOH A 399 37.031 29.946 67.989 1.00 45.29 O HETATM 1362 O HOH A 400 26.860 23.743 69.077 1.00 54.62 O HETATM 1363 O HOH A 401 32.441 23.910 57.270 1.00 45.17 O HETATM 1364 O HOH A 402 53.018 15.290 63.006 1.00 50.52 O HETATM 1365 O HOH A 403 64.219 15.162 71.370 1.00 52.85 O HETATM 1366 O HOH A 404 47.508 25.997 69.498 1.00 54.53 O HETATM 1367 O HOH A 405 24.950 22.554 69.895 1.00 47.27 O HETATM 1368 O HOH A 406 28.670 23.688 74.820 1.00 58.37 O HETATM 1369 O HOH A 407 48.872 5.854 64.507 1.00 46.33 O HETATM 1370 O HOH A 408 24.887 17.937 65.573 1.00 39.57 O HETATM 1371 O HOH A 409 24.236 5.345 68.119 1.00 39.95 O HETATM 1372 O HOH A 410 43.889 26.011 66.257 1.00 40.43 O HETATM 1373 O HOH A 411 34.960 1.795 77.359 1.00 45.35 O HETATM 1374 O HOH A 412 24.789 11.178 53.148 1.00 48.62 O HETATM 1375 O HOH A 413 38.150 4.285 79.757 1.00 38.77 O CONECT 1242 1243 1244 1245 1246 CONECT 1243 1242 CONECT 1244 1242 CONECT 1245 1242 CONECT 1246 1242 CONECT 1247 1248 1249 1250 1251 CONECT 1248 1247 CONECT 1249 1247 CONECT 1250 1247 CONECT 1251 1247 CONECT 1252 1255 1256 CONECT 1253 1254 CONECT 1254 1253 1255 CONECT 1255 1252 1254 1262 CONECT 1256 1252 1258 1261 CONECT 1257 1259 1261 CONECT 1258 1256 1260 1262 CONECT 1259 1257 1260 CONECT 1260 1258 1259 CONECT 1261 1256 1257 CONECT 1262 1255 1258 MASTER 385 0 3 2 14 0 5 6 1324 1 21 12 END