HEADER CYTOKINE 09-FEB-24 8RYK
TITLE IL-1BETA IN COMPLEX WITH MACROCYCLIC PEPTIDE HIT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INTERLEUKIN-1 BETA;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: FAB LIGHT-CHAIN;
COMPND 5 SYNONYM: IL-1 BETA,CATABOLIN;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: MATURE HUMAN INTERLEUKIN-1BETA;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: MACROCYCLIC PEPTIDE;
COMPND 10 CHAIN: C, D;
COMPND 11 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;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 11 ORGANISM_TAXID: 32630
KEYWDS PEPTIDE DISCOVERY PLATFORM, CYTOKINE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.-M.RONDEAU,S.LEHMANN
REVDAT 2 05-JUN-24 8RYK 1 JRNL
REVDAT 1 22-MAY-24 8RYK 0
JRNL AUTH A.VULPETTI,J.M.RONDEAU,M.H.BELLANCE,J.BLANK,R.BOESCH,
JRNL AUTH 2 A.BOETTCHER,F.BORNANCIN,S.BUHR,L.E.CONNOR,C.E.DUMELIN,
JRNL AUTH 3 O.ESSER,M.HEDIGER,S.HINTERMANN,U.HOMMEL,E.KOCH,G.LAPOINTE,
JRNL AUTH 4 L.LEDER,S.LEHMANN,P.LEHR,P.MEIER,L.MULLER,D.OSTERMEIER,
JRNL AUTH 5 P.RAMAGE,S.SCHIEBEL-HADDAD,A.B.SMITH,A.STOJANOVIC,
JRNL AUTH 6 J.VELCICKY,R.YAMAMOTO,K.HURTH
JRNL TITL LIGANDABILITY ASSESSMENT OF IL-1 BETA BY INTEGRATED HIT
JRNL TITL 2 IDENTIFICATION APPROACHES.
JRNL REF J.MED.CHEM. V. 67 8141 2024
JRNL REFN ISSN 0022-2623
JRNL PMID 38728572
JRNL DOI 10.1021/ACS.JMEDCHEM.4C00240
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH U.HOMMEL,K.HURTH,J.M.RONDEAU,A.VULPETTI,D.OSTERMEIER,
REMARK 1 AUTH 2 A.BOETTCHER,J.P.BRADY,M.HEDIGER,S.LEHMANN,E.KOCH,
REMARK 1 AUTH 3 A.BLECHSCHMIDT,R.YAMAMOTO,V.TUNDO DOTTORELLO,
REMARK 1 AUTH 4 S.HAENNI-HOLZINGER,C.KAISER,P.LEHR,A.LINGEL,L.MUREDDU,
REMARK 1 AUTH 5 C.SCHLEBERGER,J.BLANK,P.RAMAGE,F.FREULER,J.EDER,F.BORNANCIN
REMARK 1 TITL DISCOVERY OF A SELECTIVE AND BIOLOGICALLY ACTIVE
REMARK 1 TITL 2 LOW-MOLECULAR WEIGHT ANTAGONIST OF HUMAN INTERLEUKIN-1BETA.
REMARK 1 REF NAT COMMUN V. 14 5497 2023
REMARK 1 REFN ESSN 2041-1723
REMARK 1 PMID 37679328
REMARK 1 DOI 10.1038/S41467-023-41190-0
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.7
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.41
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 30168
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) : 0.211
REMARK 3 R VALUE (WORKING SET) : 0.209
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1509
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 50
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.81
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 604
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2248
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 574
REMARK 3 BIN R VALUE (WORKING SET) : 0.2230
REMARK 3 BIN FREE R VALUE : 0.2563
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.97
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2727
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 185
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.47
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.31470
REMARK 3 B22 (A**2) : -2.10310
REMARK 3 B33 (A**2) : 1.78840
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.280
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.155
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.141
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.149
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.138
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 2797 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 3778 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 952 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES : 471 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 2797 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 337 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 3135 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.23
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.06
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.56
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 22.7376 -5.1545 -6.1266
REMARK 3 T TENSOR
REMARK 3 T11: -0.2134 T22: 0.1240
REMARK 3 T33: -0.0753 T12: 0.0287
REMARK 3 T13: 0.0078 T23: 0.0477
REMARK 3 L TENSOR
REMARK 3 L11: 2.4927 L22: 1.5215
REMARK 3 L33: 1.9364 L12: -0.2071
REMARK 3 L13: -0.2745 L23: 0.5741
REMARK 3 S TENSOR
REMARK 3 S11: -0.1249 S12: -0.2851 S13: -0.1434
REMARK 3 S21: 0.1250 S22: 0.1268 S23: 0.0994
REMARK 3 S31: 0.0586 S32: 0.0411 S33: -0.0020
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: { B|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 51.9986 5.9057 -7.4989
REMARK 3 T TENSOR
REMARK 3 T11: -0.2249 T22: 0.1459
REMARK 3 T33: -0.0495 T12: 0.0107
REMARK 3 T13: 0.0046 T23: 0.0276
REMARK 3 L TENSOR
REMARK 3 L11: 3.3667 L22: 1.1400
REMARK 3 L33: 2.0681 L12: 0.8912
REMARK 3 L13: 0.8713 L23: 0.0856
REMARK 3 S TENSOR
REMARK 3 S11: -0.1312 S12: 0.3819 S13: -0.0542
REMARK 3 S21: -0.0717 S22: -0.0424 S23: -0.0412
REMARK 3 S31: -0.0495 S32: 0.1908 S33: 0.1736
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 8RYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-24.
REMARK 100 THE DEPOSITION ID IS D_1292136519.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-JUL-19
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000040
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 OCT. 15, 2015
REMARK 200 DATA SCALING SOFTWARE : XSCALE OCT. 15, 2015
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30169
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 51.601
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 6.500
REMARK 200 R MERGE (I) : 0.10200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 6.20
REMARK 200 R MERGE FOR SHELL (I) : 1.74000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.110
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER 2.8.2
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.15
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE PH 5.0, 1.6M AMMONIUM
REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-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 29.38850
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.10950
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.69700
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.10950
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.38850
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.69700
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1360 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9250 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9390 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D
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 LYS C 17
REMARK 465 NH2 C 18
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 TRP C 3 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES
REMARK 500 TRP C 13 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES
REMARK 500 ASP D 3 CB - CG - OD2 ANGL. DEV. = 5.5 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 -105.64 58.43
REMARK 500 PHE A 117 78.12 -117.68
REMARK 500 ASP B 75 -105.03 58.74
REMARK 500 PHE B 117 78.33 -118.54
REMARK 500
REMARK 500 REMARK: NULL
DBREF 8RYK A 1 153 UNP P01584 IL1B_HUMAN 117 269
DBREF 8RYK B 1 153 UNP P01584 IL1B_HUMAN 117 269
DBREF 8RYK C 2 18 PDB 8RYK 8RYK 2 18
DBREF 8RYK D 1 17 PDB 8RYK 8RYK 1 17
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
SEQRES 1 B 153 ALA PRO VAL ARG SER LEU ASN CYS THR LEU ARG ASP SER
SEQRES 2 B 153 GLN GLN LYS SER LEU VAL MET SER GLY PRO TYR GLU LEU
SEQRES 3 B 153 LYS ALA LEU HIS LEU GLN GLY GLN ASP MET GLU GLN GLN
SEQRES 4 B 153 VAL VAL PHE SER MET SER PHE VAL GLN GLY GLU GLU SER
SEQRES 5 B 153 ASN ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLU LYS
SEQRES 6 B 153 ASN LEU TYR LEU SER CYS VAL LEU LYS ASP ASP LYS PRO
SEQRES 7 B 153 THR LEU GLN LEU GLU SER VAL ASP PRO LYS ASN TYR PRO
SEQRES 8 B 153 LYS LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS ILE
SEQRES 9 B 153 GLU ILE ASN ASN LYS LEU GLU PHE GLU SER ALA GLN PHE
SEQRES 10 B 153 PRO ASN TRP TYR ILE SER THR SER GLN ALA GLU ASN MET
SEQRES 11 B 153 PRO VAL PHE LEU GLY GLY THR LYS GLY GLY GLN ASP ILE
SEQRES 12 B 153 THR ASP PHE THR MET GLN PHE VAL SER SER
SEQRES 1 C 17 PHE TRP ASP SER TRP GLY TYR TRP TYR GLY PRO TRP ASP
SEQRES 2 C 17 CCS GLY LYS NH2
SEQRES 1 D 17 PHE TRP ASP SER TRP GLY TYR TRP TYR GLY PRO TRP ASP
SEQRES 2 D 17 CCS GLY LYS NH2
HET CCS C 15 9
HET CCS D 14 9
HET NH2 D 17 1
HETNAM CCS CARBOXYMETHYLATED CYSTEINE
HETNAM NH2 AMINO GROUP
FORMUL 3 CCS 2(C5 H9 N O4 S)
FORMUL 4 NH2 H2 N
FORMUL 5 HOH *185(H2 O)
HELIX 1 AA1 ASP A 35 GLN A 39 5 5
HELIX 2 AA2 LYS A 63 LYS A 65 5 3
HELIX 3 AA3 GLU A 96 PHE A 99 5 4
HELIX 4 AA4 GLN B 32 GLN B 39 5 8
HELIX 5 AA5 LYS B 63 LYS B 65 5 3
HELIX 6 AA6 GLU B 96 PHE B 99 5 4
SHEET 1 AA1 6 LYS A 77 SER A 84 0
SHEET 2 AA1 6 LEU A 67 LYS A 74 -1 N SER A 70 O GLN A 81
SHEET 3 AA1 6 LYS A 55 LEU A 62 -1 N LEU A 62 O LEU A 67
SHEET 4 AA1 6 PHE A 42 PHE A 46 -1 N SER A 43 O GLY A 61
SHEET 5 AA1 6 ARG A 4 ASP A 12 -1 N LEU A 6 O MET A 44
SHEET 6 AA1 6 TRP C 9 TYR C 10 -1 O TRP C 9 N SER A 5
SHEET 1 AA2 8 LYS A 77 SER A 84 0
SHEET 2 AA2 8 LEU A 67 LYS A 74 -1 N SER A 70 O GLN A 81
SHEET 3 AA2 8 LYS A 55 LEU A 62 -1 N LEU A 62 O LEU A 67
SHEET 4 AA2 8 PHE A 101 ILE A 106 -1 O PHE A 101 N VAL A 58
SHEET 5 AA2 8 LYS A 109 SER A 114 -1 O GLU A 113 N ASN A 102
SHEET 6 AA2 8 PHE A 146 PHE A 150 -1 O PHE A 146 N LEU A 110
SHEET 7 AA2 8 ARG A 4 ASP A 12 -1 N ARG A 11 O THR A 147
SHEET 8 AA2 8 TRP C 9 TYR C 10 -1 O TRP C 9 N SER A 5
SHEET 1 AA3 3 SER A 17 MET A 20 0
SHEET 2 AA3 3 LEU A 26 LEU A 29 -1 O LYS A 27 N VAL A 19
SHEET 3 AA3 3 MET A 130 PRO A 131 -1 O MET A 130 N ALA A 28
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
SHEET 1 AA5 6 LYS B 77 SER B 84 0
SHEET 2 AA5 6 LEU B 67 LYS B 74 -1 N SER B 70 O GLN B 81
SHEET 3 AA5 6 LYS B 55 LEU B 62 -1 N LEU B 62 O LEU B 67
SHEET 4 AA5 6 PHE B 42 PHE B 46 -1 N SER B 43 O GLY B 61
SHEET 5 AA5 6 ARG B 4 ASP B 12 -1 N LEU B 6 O MET B 44
SHEET 6 AA5 6 TRP D 8 TYR D 9 -1 O TRP D 8 N SER B 5
SHEET 1 AA6 8 LYS B 77 SER B 84 0
SHEET 2 AA6 8 LEU B 67 LYS B 74 -1 N SER B 70 O GLN B 81
SHEET 3 AA6 8 LYS B 55 LEU B 62 -1 N LEU B 62 O LEU B 67
SHEET 4 AA6 8 PHE B 101 ILE B 106 -1 O PHE B 101 N VAL B 58
SHEET 5 AA6 8 LYS B 109 SER B 114 -1 O GLU B 113 N ASN B 102
SHEET 6 AA6 8 PHE B 146 PHE B 150 -1 O PHE B 146 N LEU B 110
SHEET 7 AA6 8 ARG B 4 ASP B 12 -1 N ARG B 11 O THR B 147
SHEET 8 AA6 8 TRP D 8 TYR D 9 -1 O TRP D 8 N SER B 5
SHEET 1 AA7 3 SER B 17 MET B 20 0
SHEET 2 AA7 3 LEU B 26 LEU B 29 -1 O LYS B 27 N VAL B 19
SHEET 3 AA7 3 MET B 130 PRO B 131 -1 O MET B 130 N ALA B 28
SHEET 1 AA8 2 TYR B 121 SER B 123 0
SHEET 2 AA8 2 PHE B 133 GLY B 135 -1 O PHE B 133 N SER B 123
LINK N PHE C 2 CE CCS C 15 1555 1555 1.35
LINK C ASP C 14 N CCS C 15 1555 1555 1.36
LINK C CCS C 15 N GLY C 16 1555 1555 1.36
LINK N PHE D 1 CE CCS D 14 1555 1555 1.35
LINK C ASP D 13 N CCS D 14 1555 1555 1.36
LINK C CCS D 14 N GLY D 15 1555 1555 1.36
LINK C LYS D 16 N NH2 D 17 1555 1555 1.36
CISPEP 1 TYR A 90 PRO A 91 0 -3.33
CISPEP 2 TYR B 90 PRO B 91 0 -4.53
CRYST1 58.777 67.394 80.219 90.00 90.00 90.00 P 21 21 21 8
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 0.017013 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014838 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012466 0.00000