HEADER IMMUNE SYSTEM 15-JAN-24 8RPB
TITLE STRUCTURE OF S79 FAB IN COMPLEX WITH IGV DOMAIN OF HUMAN PD-L1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HEAVY CHAIN OF S79 FAB;
COMPND 3 CHAIN: H;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: LIGHT CHAIN OF S79 FAB;
COMPND 7 CHAIN: L;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1;
COMPND 11 CHAIN: P;
COMPND 12 SYNONYM: PD-L1,PDCD1 LIGAND 1,PROGRAMMED DEATH LIGAND 1,HPD-L1,B7
COMPND 13 HOMOLOG 1,B7-H1;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_TAXID: 9606;
SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 6 MOL_ID: 2;
SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 8 ORGANISM_TAXID: 9606;
SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 11 MOL_ID: 3;
SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 13 ORGANISM_COMMON: HUMAN;
SOURCE 14 ORGANISM_TAXID: 9606;
SOURCE 15 GENE: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1;
SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS IMMUNE SYSTEM, FAB
EXPDTA X-RAY DIFFRACTION
AUTHOR A.SVENSSON,V.KELPSAS,M.LAURSEN,N.ROSE
REVDAT 2 16-OCT-24 8RPB 1 REMARK
REVDAT 1 19-JUN-24 8RPB 0
JRNL AUTH P.MALINGE,X.CHAUCHET,J.BOURGUIGNON,N.BOSSON,S.CALLOUD,
JRNL AUTH 2 T.BAUTZOVA,M.BORLET,M.LAURSEN,V.KELPSAS,N.ROSE,F.GUENEAU,
JRNL AUTH 3 U.RAVN,G.MAGISTRELLI,N.FISCHER
JRNL TITL STRUCTURAL ANALYSIS OF LIGHT CHAIN-DRIVEN BISPECIFIC
JRNL TITL 2 ANTIBODIES TARGETING CD47 AND PD-L1.
JRNL REF MABS V. 16 62432 2024
JRNL REFN ESSN 1942-0870
JRNL PMID 38849989
JRNL DOI 10.1080/19420862.2024.2362432
REMARK 2
REMARK 2 RESOLUTION. 2.79 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.8 (8-JUN-2022)
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) : 2.79
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.24
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 28249
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) : 0.230
REMARK 3 R VALUE (WORKING SET) : 0.229
REMARK 3 FREE R VALUE : 0.251
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 1385
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 : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.79
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.81
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.51
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL
REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.3414
REMARK 3 BIN FREE R VALUE : 0.3519
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 24
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 : 4124
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 49
REMARK 3 SOLVENT ATOMS : 17
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 119.0
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -3.02030
REMARK 3 B22 (A**2) : -3.02030
REMARK 3 B33 (A**2) : 6.04060
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) : 0.410
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.383
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.266
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.385
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.269
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 : 0.937
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 4263 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 5799 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1397 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES : 703 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 4263 ; 10.000 ; 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 : 558 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : 2 ; 1.000 ; HARMONIC
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 2908 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 0.96
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.26
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.79
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { H|1 - H|116 L|1 - L|113 }
REMARK 3 ORIGIN FOR THE GROUP (A): -17.4374 -74.7604 -9.3984
REMARK 3 T TENSOR
REMARK 3 T11: -0.2457 T22: 0.1993
REMARK 3 T33: 0.1313 T12: 0.1743
REMARK 3 T13: -0.1932 T23: -0.0256
REMARK 3 L TENSOR
REMARK 3 L11: 6.4416 L22: 2.0523
REMARK 3 L33: 2.6844 L12: -0.074
REMARK 3 L13: 0.9485 L23: 0.7404
REMARK 3 S TENSOR
REMARK 3 S11: -0.397 S12: -0.1112 S13: -0.3155
REMARK 3 S21: -0.1112 S22: -0.0355 S23: 0.5856
REMARK 3 S31: -0.3155 S32: 0.5856 S33: 0.4326
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: { H|117 - H|218 L|114 - L|215 }
REMARK 3 ORIGIN FOR THE GROUP (A): -40.2809 -60.9584 12.792
REMARK 3 T TENSOR
REMARK 3 T11: 0.0284 T22: 0.5367
REMARK 3 T33: -0.2772 T12: 0.8038
REMARK 3 T13: -0.3664 T23: -0.5064
REMARK 3 L TENSOR
REMARK 3 L11: 6.8902 L22: 8.32
REMARK 3 L33: 5.0447 L12: -0.876
REMARK 3 L13: 1.3021 L23: 2.2508
REMARK 3 S TENSOR
REMARK 3 S11: -1.2115 S12: 1.5701 S13: -0.434
REMARK 3 S21: 1.5701 S22: 1.191 S23: -0.2982
REMARK 3 S31: -0.434 S32: -0.2982 S33: 0.0205
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: { P|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 2.3222 -71.1313 -29.0013
REMARK 3 T TENSOR
REMARK 3 T11: -0.7768 T22: 1.1164
REMARK 3 T33: -0.3712 T12: -0.1817
REMARK 3 T13: -0.0474 T23: 0.8076
REMARK 3 L TENSOR
REMARK 3 L11: 11.6712 L22: 6.8222
REMARK 3 L33: 8.8733 L12: -2.5393
REMARK 3 L13: 1.6282 L23: -2.3429
REMARK 3 S TENSOR
REMARK 3 S11: -0.6184 S12: -0.6389 S13: -0.7085
REMARK 3 S21: -0.6389 S22: -0.2701 S23: 2.4728
REMARK 3 S31: -0.7085 S32: 2.4728 S33: 0.8885
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 8RPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JAN-24.
REMARK 100 THE DEPOSITION ID IS D_1292135379.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-JUL-22
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : MAX IV
REMARK 200 BEAMLINE : BIOMAX
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28276
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790
REMARK 200 RESOLUTION RANGE LOW (A) : 48.240
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 24.00
REMARK 200 R MERGE (I) : 0.20500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.94
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1
REMARK 200 DATA REDUNDANCY IN SHELL : 23.90
REMARK 200 R MERGE FOR SHELL (I) : 3.08900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 70.82
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.21
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.0, 1.6M LI2SO4, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z
REMARK 290 5555 Y,-X+Y,Z+2/3
REMARK 290 6555 X-Y,X,Z+1/3
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+2/3
REMARK 290 11555 -X+Y,Y,-Z
REMARK 290 12555 X,X-Y,-Z+1/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.49133
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.74567
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.49133
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.74567
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.49133
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 36.74567
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 73.49133
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 36.74567
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6840 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 24430 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, P
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 S SO4 H 306 LIES ON A SPECIAL POSITION.
REMARK 375 O1 SO4 H 306 LIES ON A SPECIAL POSITION.
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 CYS H 219
REMARK 465 ASP H 220
REMARK 465 LYS H 221
REMARK 465 THR H 222
REMARK 465 HIS H 223
REMARK 465 CYS L 216
REMARK 465 SER L 217
REMARK 465 MET P 17
REMARK 465 ALA P 132
REMARK 465 PRO P 133
REMARK 465 GLY P 134
REMARK 465 SER P 135
REMARK 465 HIS P 136
REMARK 465 HIS P 137
REMARK 465 HIS P 138
REMARK 465 HIS P 139
REMARK 465 HIS P 140
REMARK 465 HIS P 141
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 TYR H 100 74.14 -153.18
REMARK 500 SER H 135 10.73 90.10
REMARK 500 ALA L 53 -34.90 65.85
REMARK 500 ASN L 71 51.29 -102.00
REMARK 500 GLN L 113 124.92 -30.16
REMARK 500 ASP L 156 61.17 23.92
REMARK 500 SER L 157 -19.64 104.45
REMARK 500 LYS P 46 -27.13 72.66
REMARK 500 GLN P 47 53.62 -110.84
REMARK 500 GLN P 83 -5.28 66.46
REMARK 500 TYR P 118 71.94 -157.68
REMARK 500
REMARK 500 REMARK: NULL
DBREF 8RPB H 1 223 PDB 8RPB 8RPB 1 223
DBREF 8RPB L 1 217 PDB 8RPB 8RPB 1 217
DBREF 8RPB P 18 133 UNP Q9NZQ7 PD1L1_HUMAN 18 133
SEQADV 8RPB MET P 17 UNP Q9NZQ7 INITIATING METHIONINE
SEQADV 8RPB GLY P 134 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 8RPB SER P 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 8RPB HIS P 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 8RPB HIS P 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 8RPB HIS P 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 8RPB HIS P 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 8RPB HIS P 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 8RPB HIS P 141 UNP Q9NZQ7 EXPRESSION TAG
SEQRES 1 H 223 GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU VAL GLN
SEQRES 2 H 223 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY
SEQRES 3 H 223 PHE THR PHE SER SER TYR ALA MET SER TRP VAL ARG GLN
SEQRES 4 H 223 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ALA ILE SER
SEQRES 5 H 223 GLY SER GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS
SEQRES 6 H 223 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR
SEQRES 7 H 223 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR
SEQRES 8 H 223 ALA VAL TYR TYR CYS ALA LYS SER TYR GLY ALA PHE ASP
SEQRES 9 H 223 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA
SEQRES 10 H 223 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER
SEQRES 11 H 223 SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS
SEQRES 12 H 223 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER
SEQRES 13 H 223 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE
SEQRES 14 H 223 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER
SEQRES 15 H 223 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN
SEQRES 16 H 223 THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR
SEQRES 17 H 223 LYS VAL ASP LYS ARG VAL GLU PRO LYS SER CYS ASP LYS
SEQRES 18 H 223 THR HIS
SEQRES 1 L 217 GLN SER ALA LEU THR GLN PRO ALA SER VAL SER GLY SER
SEQRES 2 L 217 PRO GLY GLN SER ILE THR ILE SER CYS THR GLY THR SER
SEQRES 3 L 217 SER ASP VAL PHE ARG PRO PRO LEU VAL SER TRP TYR GLN
SEQRES 4 L 217 GLN HIS PRO GLY LYS ALA PRO LYS LEU MET ILE TYR PHE
SEQRES 5 L 217 ALA SER LEU ARG PRO SER GLY VAL SER ASN ARG PHE SER
SEQRES 6 L 217 GLY SER LYS SER GLY ASN THR ALA SER LEU THR ILE SER
SEQRES 7 L 217 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS SER
SEQRES 8 L 217 SER TRP ASP HIS THR GLY ASP GLY HIS VAL PHE GLY GLY
SEQRES 9 L 217 GLY THR LYS LEU THR VAL LEU GLY GLN PRO LYS ALA ALA
SEQRES 10 L 217 PRO SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU
SEQRES 11 L 217 GLN ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP
SEQRES 12 L 217 PHE TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP
SEQRES 13 L 217 SER SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO
SEQRES 14 L 217 SER LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR
SEQRES 15 L 217 LEU SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER
SEQRES 16 L 217 TYR SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU
SEQRES 17 L 217 LYS THR VAL ALA PRO THR GLU CYS SER
SEQRES 1 P 125 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL
SEQRES 2 P 125 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE
SEQRES 3 P 125 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL
SEQRES 4 P 125 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL
SEQRES 5 P 125 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR
SEQRES 6 P 125 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU
SEQRES 7 P 125 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN
SEQRES 8 P 125 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY
SEQRES 9 P 125 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO
SEQRES 10 P 125 GLY SER HIS HIS HIS HIS HIS HIS
HET CL H 301 1
HET GOL H 302 6
HET GOL H 303 6
HET GOL H 304 6
HET SO4 H 305 5
HET SO4 H 306 5
HET SO4 L 301 5
HET SO4 L 302 5
HET SO4 L 303 5
HET SO4 P 201 5
HETNAM CL CHLORIDE ION
HETNAM GOL GLYCEROL
HETNAM SO4 SULFATE ION
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 4 CL CL 1-
FORMUL 5 GOL 3(C3 H8 O3)
FORMUL 8 SO4 6(O4 S 2-)
FORMUL 14 HOH *17(H2 O)
HELIX 1 AA1 THR H 28 TYR H 32 5 5
HELIX 2 AA2 ARG H 87 THR H 91 5 5
HELIX 3 AA3 SER H 130 THR H 134 5 5
HELIX 4 AA4 SER H 159 ALA H 161 5 3
HELIX 5 AA5 LYS H 204 ASN H 207 5 4
HELIX 6 AA6 ARG L 31 PRO L 33 5 3
HELIX 7 AA7 GLN L 81 GLU L 85 5 5
HELIX 8 AA8 SER L 126 ALA L 132 1 7
HELIX 9 AA9 THR L 186 SER L 192 1 7
HELIX 10 AB1 ASP P 49 LEU P 53 5 5
HELIX 11 AB2 LEU P 74 GLN P 77 5 4
HELIX 12 AB3 HIS P 78 ARG P 82 5 5
HELIX 13 AB4 LYS P 89 LEU P 94 5 6
HELIX 14 AB5 LYS P 105 ALA P 109 5 5
SHEET 1 AA1 4 GLN H 3 SER H 7 0
SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 25 N GLN H 3
SHEET 3 AA1 4 THR H 78 MET H 83 -1 O MET H 83 N LEU H 18
SHEET 4 AA1 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80
SHEET 1 AA2 6 GLY H 10 VAL H 12 0
SHEET 2 AA2 6 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12
SHEET 3 AA2 6 ALA H 92 SER H 99 -1 N TYR H 94 O THR H 110
SHEET 4 AA2 6 ALA H 33 GLN H 39 -1 N VAL H 37 O TYR H 95
SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38
SHEET 6 AA2 6 THR H 58 TYR H 60 -1 O TYR H 59 N ALA H 50
SHEET 1 AA3 4 GLY H 10 VAL H 12 0
SHEET 2 AA3 4 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12
SHEET 3 AA3 4 ALA H 92 SER H 99 -1 N TYR H 94 O THR H 110
SHEET 4 AA3 4 PHE H 103 TRP H 106 -1 O TYR H 105 N LYS H 98
SHEET 1 AA4 4 SER H 123 LEU H 127 0
SHEET 2 AA4 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125
SHEET 3 AA4 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148
SHEET 4 AA4 4 VAL H 166 THR H 168 -1 N HIS H 167 O VAL H 184
SHEET 1 AA5 4 SER H 123 LEU H 127 0
SHEET 2 AA5 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125
SHEET 3 AA5 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148
SHEET 4 AA5 4 VAL H 172 LEU H 173 -1 N VAL H 172 O SER H 180
SHEET 1 AA6 3 THR H 154 TRP H 157 0
SHEET 2 AA6 3 ILE H 198 HIS H 203 -1 O ASN H 200 N SER H 156
SHEET 3 AA6 3 THR H 208 ARG H 213 -1 O VAL H 210 N VAL H 201
SHEET 1 AA7 5 SER L 9 GLY L 12 0
SHEET 2 AA7 5 THR L 106 VAL L 110 1 O THR L 109 N VAL L 10
SHEET 3 AA7 5 ASP L 87 TRP L 93 -1 N TYR L 88 O THR L 106
SHEET 4 AA7 5 VAL L 35 GLN L 40 -1 N GLN L 40 O ASP L 87
SHEET 5 AA7 5 LYS L 47 ILE L 50 -1 O MET L 49 N TRP L 37
SHEET 1 AA8 4 SER L 9 GLY L 12 0
SHEET 2 AA8 4 THR L 106 VAL L 110 1 O THR L 109 N VAL L 10
SHEET 3 AA8 4 ASP L 87 TRP L 93 -1 N TYR L 88 O THR L 106
SHEET 4 AA8 4 HIS L 100 PHE L 102 -1 O VAL L 101 N SER L 92
SHEET 1 AA9 3 ILE L 18 CYS L 22 0
SHEET 2 AA9 3 THR L 72 ILE L 77 -1 O ALA L 73 N CYS L 22
SHEET 3 AA9 3 PHE L 64 SER L 69 -1 N SER L 65 O THR L 76
SHEET 1 AB1 4 SER L 119 PHE L 123 0
SHEET 2 AB1 4 ALA L 135 PHE L 144 -1 O LEU L 140 N THR L 121
SHEET 3 AB1 4 TYR L 177 LEU L 185 -1 O SER L 181 N CYS L 139
SHEET 4 AB1 4 VAL L 164 THR L 166 -1 N GLU L 165 O TYR L 182
SHEET 1 AB2 4 SER L 119 PHE L 123 0
SHEET 2 AB2 4 ALA L 135 PHE L 144 -1 O LEU L 140 N THR L 121
SHEET 3 AB2 4 TYR L 177 LEU L 185 -1 O SER L 181 N CYS L 139
SHEET 4 AB2 4 SER L 170 LYS L 171 -1 N SER L 170 O ALA L 178
SHEET 1 AB3 4 SER L 158 VAL L 160 0
SHEET 2 AB3 4 THR L 150 ALA L 155 -1 N ALA L 155 O SER L 158
SHEET 3 AB3 4 TYR L 196 HIS L 202 -1 O GLN L 199 N ALA L 152
SHEET 4 AB3 4 SER L 205 VAL L 211 -1 O VAL L 207 N VAL L 200
SHEET 1 AB4 6 LEU P 27 GLU P 31 0
SHEET 2 AB4 6 ALA P 121 ASN P 131 1 O LYS P 129 N VAL P 30
SHEET 3 AB4 6 GLY P 110 SER P 117 -1 N TYR P 112 O ILE P 126
SHEET 4 AB4 6 ILE P 54 MET P 59 -1 N TYR P 56 O MET P 115
SHEET 5 AB4 6 LYS P 62 VAL P 68 -1 O ILE P 64 N TRP P 57
SHEET 6 AB4 6 GLU P 71 GLU P 72 -1 O GLU P 71 N VAL P 68
SHEET 1 AB5 3 MET P 36 LYS P 41 0
SHEET 2 AB5 3 ASN P 96 ILE P 101 -1 O ALA P 97 N CYS P 40
SHEET 3 AB5 3 ALA P 85 LEU P 87 -1 N ARG P 86 O GLN P 100
SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.06
SSBOND 2 CYS H 143 CYS H 199 1555 1555 2.04
SSBOND 3 CYS L 22 CYS L 90 1555 1555 2.04
SSBOND 4 CYS L 139 CYS L 198 1555 1555 2.04
SSBOND 5 CYS P 40 CYS P 114 1555 1555 2.03
CISPEP 1 PHE H 149 PRO H 150 0 -5.30
CISPEP 2 GLU H 151 PRO H 152 0 6.96
CISPEP 3 TYR L 145 PRO L 146 0 -1.58
CRYST1 185.852 185.852 110.237 90.00 90.00 120.00 P 62 2 2 12
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 0.005381 0.003107 0.000000 0.00000
SCALE2 0.000000 0.006213 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009071 0.00000