HEADER CELL CYCLE 05-FEB-20 6VQN
TITLE CO-CRYSTAL STRUCTURE OF HUMAN PD-L1 COMPLEXED WITH COMPOUND A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1;
COMPND 3 CHAIN: A, B, C;
COMPND 4 SYNONYM: HPD-L1,B7 HOMOLOG 1,B7-H1;
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: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28
KEYWDS COMPLEX, CELL CYCLE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.WHITE,D.LAKSHMINARASIMHAN,C.LEO,R.K.SUTO
REVDAT 4 16-OCT-24 6VQN 1 REMARK
REVDAT 3 11-OCT-23 6VQN 1 REMARK
REVDAT 2 10-MAR-21 6VQN 1 JRNL
REVDAT 1 20-JAN-21 6VQN 0
JRNL AUTH J.J.PARK,E.P.THI,V.H.CARPIO,Y.BI,A.G.COLE,B.D.DORSEY,K.FAN,
JRNL AUTH 2 T.HARASYM,C.L.IOTT,S.KADHIM,J.H.KIM,A.C.H.LEE,D.NGUYEN,
JRNL AUTH 3 B.S.PARATALA,R.QIU,A.WHITE,D.LAKSHMINARASIMHAN,C.LEO,
JRNL AUTH 4 R.K.SUTO,R.RIJNBRAND,S.TANG,M.J.SOFIA,C.B.MOORE
JRNL TITL CHECKPOINT INHIBITION THROUGH SMALL MOLECULE-INDUCED
JRNL TITL 2 INTERNALIZATION OF PROGRAMMED DEATH-LIGAND 1.
JRNL REF NAT COMMUN V. 12 1222 2021
JRNL REFN ESSN 2041-1723
JRNL PMID 33619272
JRNL DOI 10.1038/S41467-021-21410-1
REMARK 2
REMARK 2 RESOLUTION. 2.49 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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.90
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 23114
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) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.177
REMARK 3 FREE R VALUE : 0.228
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600
REMARK 3 FREE R VALUE TEST SET COUNT : 1117
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) : 2.49
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1703
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.83
REMARK 3 BIN R VALUE (WORKING SET) : 0.3280
REMARK 3 BIN FREE R VALUE SET COUNT : 67
REMARK 3 BIN FREE R VALUE : 0.3540
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2912
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 63
REMARK 3 SOLVENT ATOMS : 139
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.87
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -3.24000
REMARK 3 B22 (A**2) : -1.87000
REMARK 3 B33 (A**2) : 5.12000
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): 0.243
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.357
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3037 ; 0.012 ; 0.013
REMARK 3 BOND LENGTHS OTHERS (A): 2838 ; 0.004 ; 0.017
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4107 ; 1.663 ; 1.667
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6566 ; 1.378 ; 1.603
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 6.585 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;35.916 ;23.182
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 529 ;20.813 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;27.130 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 383 ; 0.067 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3353 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 623 ; 0.001 ; 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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 : NULL
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 6VQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-20.
REMARK 100 THE DEPOSITION ID IS D_1000246884.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-OCT-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALBA
REMARK 200 BEAMLINE : XALOC
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97928
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 : 24239
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490
REMARK 200 RESOLUTION RANGE LOW (A) : 80.580
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 7.300
REMARK 200 R MERGE (I) : 0.09700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : 7.70
REMARK 200 R MERGE FOR SHELL (I) : 1.16300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 4ZQK
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 68.17
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NACITRATE, PH 6.5 AND 22% (W/V)
REMARK 280 PEG 3000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
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 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.29250
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.29250
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 1.000000 0.000000 0.000000 49.50150
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 86.08650
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.50150
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 86.08650
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.29250
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.50150
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 86.08650
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.29250
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.50150
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 86.08650
REMARK 290 SMTRY3 8 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 APPLY THE FOLLOWING TO CHAINS: A, B
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 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 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 MET A 17
REMARK 465 GLU A 139
REMARK 465 HIS A 140
REMARK 465 HIS A 141
REMARK 465 HIS A 142
REMARK 465 HIS A 143
REMARK 465 HIS A 144
REMARK 465 HIS A 145
REMARK 465 MET B 17
REMARK 465 ALA B 137
REMARK 465 LEU B 138
REMARK 465 GLU B 139
REMARK 465 HIS B 140
REMARK 465 HIS B 141
REMARK 465 HIS B 142
REMARK 465 HIS B 143
REMARK 465 HIS B 144
REMARK 465 HIS B 145
REMARK 465 MET C 17
REMARK 465 HIS C 143
REMARK 465 HIS C 144
REMARK 465 HIS C 145
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 LEU A 138 CG CD1 CD2
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 NH2 ARG A 86 OD2 ASP C 103 8545 2.07
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 LYS A 46 -138.91 63.09
REMARK 500 TYR A 118 90.26 -160.88
REMARK 500 LYS B 46 -121.35 62.01
REMARK 500 ASP B 103 65.28 62.23
REMARK 500 TYR B 118 87.18 -158.65
REMARK 500 LYS C 46 -119.91 51.65
REMARK 500 ASP C 61 -2.48 80.14
REMARK 500 HIS C 140 -51.04 -122.94
REMARK 500 HIS C 141 82.43 -69.98
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 241 DISTANCE = 5.82 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue R81 B 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue R81 C 201
DBREF 6VQN A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
DBREF 6VQN B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
DBREF 6VQN C 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
SEQADV 6VQN MET A 17 UNP Q9NZQ7 INITIATING METHIONINE
SEQADV 6VQN ALA A 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN ALA A 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN ALA A 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN LEU A 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN GLU A 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS A 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS A 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS A 142 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS A 143 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS A 144 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS A 145 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN MET B 17 UNP Q9NZQ7 INITIATING METHIONINE
SEQADV 6VQN ALA B 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN ALA B 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN ALA B 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN LEU B 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN GLU B 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS B 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS B 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS B 142 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS B 143 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS B 144 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS B 145 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN MET C 17 UNP Q9NZQ7 INITIATING METHIONINE
SEQADV 6VQN ALA C 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN ALA C 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN ALA C 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN LEU C 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN GLU C 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS C 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS C 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS C 142 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS C 143 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS C 144 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 6VQN HIS C 145 UNP Q9NZQ7 EXPRESSION TAG
SEQRES 1 A 129 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL
SEQRES 2 A 129 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE
SEQRES 3 A 129 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL
SEQRES 4 A 129 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL
SEQRES 5 A 129 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR
SEQRES 6 A 129 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU
SEQRES 7 A 129 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN
SEQRES 8 A 129 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY
SEQRES 9 A 129 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO
SEQRES 10 A 129 TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
SEQRES 1 B 129 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL
SEQRES 2 B 129 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE
SEQRES 3 B 129 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL
SEQRES 4 B 129 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL
SEQRES 5 B 129 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR
SEQRES 6 B 129 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU
SEQRES 7 B 129 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN
SEQRES 8 B 129 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY
SEQRES 9 B 129 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO
SEQRES 10 B 129 TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
SEQRES 1 C 129 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL
SEQRES 2 C 129 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE
SEQRES 3 C 129 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL
SEQRES 4 C 129 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL
SEQRES 5 C 129 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR
SEQRES 6 C 129 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU
SEQRES 7 C 129 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN
SEQRES 8 C 129 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY
SEQRES 9 C 129 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO
SEQRES 10 C 129 TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
HET R81 B 201 42
HET R81 C 201 21
HETNAM R81 N,N'-(2,2'-DIMETHYL[1,1'-BIPHENYL]-3,3'-DIYL)BIS(5-
HETNAM 2 R81 {[(2-HYDROXYETHYL)AMINO]METHYL}PYRIDINE-2-CARBOXAMIDE)
FORMUL 4 R81 2(C32 H36 N6 O4)
FORMUL 6 HOH *139(H2 O)
HELIX 1 AA1 ASP A 49 ALA A 52 5 4
HELIX 2 AA2 HIS A 78 ARG A 82 5 5
HELIX 3 AA3 LYS A 89 LEU A 94 5 6
HELIX 4 AA4 LYS A 105 ALA A 109 5 5
HELIX 5 AA5 ASP B 49 ALA B 52 5 4
HELIX 6 AA6 LEU B 74 GLN B 77 5 4
HELIX 7 AA7 HIS B 78 ARG B 82 5 5
HELIX 8 AA8 GLN B 91 LEU B 94 5 4
HELIX 9 AA9 LYS B 105 ALA B 109 5 5
HELIX 10 AB1 ASP C 49 ALA C 52 5 4
HELIX 11 AB2 HIS C 78 ARG C 82 5 5
HELIX 12 AB3 GLN C 91 LEU C 94 5 4
HELIX 13 AB4 LYS C 105 ALA C 109 5 5
SHEET 1 AA1 5 LEU A 27 GLU A 31 0
SHEET 2 AA1 5 ALA A 121 ASN A 131 1 O LYS A 129 N VAL A 30
SHEET 3 AA1 5 GLY A 110 SER A 117 -1 N TYR A 112 O ILE A 126
SHEET 4 AA1 5 ILE A 54 MET A 59 -1 N TYR A 56 O MET A 115
SHEET 5 AA1 5 LYS A 62 VAL A 68 -1 O PHE A 67 N VAL A 55
SHEET 1 AA2 3 MET A 36 LYS A 41 0
SHEET 2 AA2 3 ASN A 96 ILE A 101 -1 O ALA A 97 N CYS A 40
SHEET 3 AA2 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100
SHEET 1 AA3 6 LEU B 27 GLU B 31 0
SHEET 2 AA3 6 ALA B 121 ASN B 131 1 O THR B 127 N TYR B 28
SHEET 3 AA3 6 GLY B 110 SER B 117 -1 N TYR B 112 O ILE B 126
SHEET 4 AA3 6 ILE B 54 MET B 59 -1 N TYR B 56 O MET B 115
SHEET 5 AA3 6 LYS B 62 VAL B 68 -1 O PHE B 67 N VAL B 55
SHEET 6 AA3 6 GLU B 71 GLU B 72 -1 O GLU B 71 N VAL B 68
SHEET 1 AA4 3 MET B 36 LYS B 41 0
SHEET 2 AA4 3 ASN B 96 ILE B 101 -1 O ALA B 97 N CYS B 40
SHEET 3 AA4 3 ALA B 85 LEU B 87 -1 N ARG B 86 O GLN B 100
SHEET 1 AA5 6 LEU C 27 GLU C 31 0
SHEET 2 AA5 6 ALA C 121 ASN C 131 1 O LYS C 129 N TYR C 28
SHEET 3 AA5 6 GLY C 110 SER C 117 -1 N TYR C 112 O ILE C 126
SHEET 4 AA5 6 ILE C 54 MET C 59 -1 N TYR C 56 O MET C 115
SHEET 5 AA5 6 LYS C 62 VAL C 68 -1 O PHE C 67 N VAL C 55
SHEET 6 AA5 6 GLU C 71 GLU C 72 -1 O GLU C 71 N VAL C 68
SHEET 1 AA6 3 MET C 36 LYS C 41 0
SHEET 2 AA6 3 ASN C 96 ILE C 101 -1 O ILE C 101 N MET C 36
SHEET 3 AA6 3 ALA C 85 LEU C 87 -1 N ARG C 86 O GLN C 100
SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.01
SSBOND 2 CYS B 40 CYS B 114 1555 1555 2.00
SSBOND 3 CYS C 40 CYS C 114 1555 1555 2.01
LINK C R81 C 201 C R81 C 201 1555 4555 1.45
SITE 1 AC1 19 TYR A 56 MET A 115 ILE A 116 SER A 117
SITE 2 AC1 19 ALA A 121 ASP A 122 TYR A 123 TYR B 56
SITE 3 AC1 19 GLN B 66 MET B 115 ILE B 116 SER B 117
SITE 4 AC1 19 ALA B 121 ASP B 122 TYR B 123 LYS B 124
SITE 5 AC1 19 HOH B 314 HOH B 315 HOH B 317
SITE 1 AC2 11 VAL C 21 TYR C 56 MET C 115 ILE C 116
SITE 2 AC2 11 SER C 117 ALA C 121 ASP C 122 TYR C 123
SITE 3 AC2 11 HOH C 305 HOH C 318 HOH C 324
CRYST1 99.003 172.173 80.585 90.00 90.00 90.00 C 2 2 21 24
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 0.010101 0.000000 0.000000 0.00000
SCALE2 0.000000 0.005808 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012409 0.00000