HEADER IMMUNE SYSTEM 27-MAR-17 5NIU
TITLE STRUCTURE OF HUMAN PROGRAMMED CELL DEATH 1 LIGAND 1 (PD-L1) WITH LOW
TITLE 2 MOLECULAR MASS INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 SYNONYM: PROGRAMMED DEATH LIGAND 1,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;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PD-L1, PD-1, IMMUNE CHECKPOINT, IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR K.M.ZAK,P.GRUDNIK,L.SKALNIAK,G.DUBIN,T.A.HOLAK
REVDAT 3 13-NOV-24 5NIU 1 REMARK
REVDAT 2 17-JAN-24 5NIU 1 REMARK
REVDAT 1 06-DEC-17 5NIU 0
JRNL AUTH L.SKALNIAK,K.M.ZAK,K.GUZIK,K.MAGIERA,B.MUSIELAK,M.PACHOTA,
JRNL AUTH 2 B.SZELAZEK,J.KOCIK,P.GRUDNIK,M.TOMALA,S.KRZANIK,K.PYRC,
JRNL AUTH 3 A.DOMLING,G.DUBIN,T.A.HOLAK
JRNL TITL SMALL-MOLECULE INHIBITORS OF PD-1/PD-L1 IMMUNE CHECKPOINT
JRNL TITL 2 ALLEVIATE THE PD-L1-INDUCED EXHAUSTION OF T-CELLS.
JRNL REF ONCOTARGET V. 8 72167 2017
JRNL REFN ESSN 1949-2553
JRNL PMID 29069777
JRNL DOI 10.18632/ONCOTARGET.20050
REMARK 2
REMARK 2 RESOLUTION. 2.01 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.01
REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 35934
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.210
REMARK 3 R VALUE (WORKING SET) : 0.208
REMARK 3 FREE R VALUE : 0.262
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1846
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : NULL
REMARK 3 SHRINKAGE RADIUS : NULL
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.19
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.43000
REMARK 3 B22 (A**2) : -1.08000
REMARK 3 B33 (A**2) : -1.35000
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 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5NIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAR-17.
REMARK 100 THE DEPOSITION ID IS D_1200004206.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-JUL-16
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 : PETRA III, DESY
REMARK 200 BEAMLINE : P11
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37778
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010
REMARK 200 RESOLUTION RANGE LOW (A) : 46.010
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 12.70
REMARK 200 R MERGE (I) : 0.06500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7
REMARK 200 DATA REDUNDANCY IN SHELL : 12.70
REMARK 200 R MERGE FOR SHELL (I) : 0.45200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.300
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: 5C3T
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.46
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5 CONTAINING 0.2 M
REMARK 280 MAGNESIUM CHLORIDE AND 30% (W/V) PEG 4000, VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 298K
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 19.94100
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.20250
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.33650
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.20250
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.94100
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.33650
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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 HIS A 144
REMARK 465 HIS A 145
REMARK 465 HIS B 143
REMARK 465 HIS B 144
REMARK 465 HIS B 145
REMARK 465 HIS C 144
REMARK 465 HIS C 145
REMARK 465 HIS D 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 GLU A 45 CG CD OE1 OE2
REMARK 470 LYS A 46 CG CD CE NZ
REMARK 470 GLN A 47 CG CD OE1 NE2
REMARK 470 GLU A 71 CG CD OE1 OE2
REMARK 470 LEU A 74 CG CD1 CD2
REMARK 470 LYS A 75 CG CD CE NZ
REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 83 CG CD OE1 NE2
REMARK 470 HIS A 143 CG ND1 CD2 CE1 NE2
REMARK 470 GLU B 45 CG CD OE1 OE2
REMARK 470 LYS B 46 CG CD CE NZ
REMARK 470 GLN B 47 CG CD OE1 NE2
REMARK 470 GLU B 71 CG CD OE1 OE2
REMARK 470 LEU B 74 CG CD1 CD2
REMARK 470 LYS B 75 CD CE NZ
REMARK 470 ARG B 86 CD NE CZ NH1 NH2
REMARK 470 GLN B 107 CG CD OE1 NE2
REMARK 470 HIS B 142 CG ND1 CD2 CE1 NE2
REMARK 470 GLU C 45 CG CD OE1 OE2
REMARK 470 LYS C 46 CB CG CD CE NZ
REMARK 470 GLN C 47 CG CD OE1 NE2
REMARK 470 LEU C 50 CG CD1 CD2
REMARK 470 GLU C 71 CG CD OE1 OE2
REMARK 470 LYS C 75 CG CD CE NZ
REMARK 470 VAL C 76 CG1 CG2
REMARK 470 ARG C 82 CG CD NE CZ NH1 NH2
REMARK 470 LYS C 105 CG CD CE NZ
REMARK 470 HIS C 143 CG ND1 CD2 CE1 NE2
REMARK 470 GLU D 45 CG CD OE1 OE2
REMARK 470 LYS D 46 CB CG CD CE NZ
REMARK 470 GLN D 47 CG CD OE1 NE2
REMARK 470 ASN D 63 CG OD1 ND2
REMARK 470 GLU D 71 CG CD OE1 OE2
REMARK 470 LYS D 75 CG CD CE NZ
REMARK 470 GLN D 77 CD OE1 NE2
REMARK 470 ARG D 82 CG CD NE CZ NH1 NH2
REMARK 470 GLN D 83 CG CD OE1 NE2
REMARK 470 HIS D 144 CG ND1 CD2 CE1 NE2
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 GLU A 58 N CA C O CB CG CD
REMARK 480 GLU A 58 OE1 OE2
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 B 266 O HOH B 277 1.98
REMARK 500 CB GLU A 45 O HOH A 367 1.98
REMARK 500 O HOH B 224 O HOH B 277 2.00
REMARK 500 O ASP A 61 O HOH A 301 2.05
REMARK 500 NH1 ARG A 125 O HOH A 302 2.05
REMARK 500 O LEU C 138 O HIS C 141 2.09
REMARK 500 O HOH D 353 O HOH D 385 2.10
REMARK 500 OE2 GLU A 72 O HOH A 303 2.11
REMARK 500 NE2 GLN B 100 O HOH B 201 2.13
REMARK 500 O HOH C 304 O HOH C 344 2.17
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 CYS A 40 CB CYS A 40 SG -0.107
REMARK 500 GLU A 60 CD GLU A 60 OE2 0.073
REMARK 500 CYS B 40 CB CYS B 40 SG -0.158
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 CYS B 40 N - CA - CB ANGL. DEV. = -12.8 DEGREES
REMARK 500 GLU B 139 C - N - CA ANGL. DEV. = 15.2 DEGREES
REMARK 500 GLU B 139 N - CA - C ANGL. DEV. = -24.1 DEGREES
REMARK 500 MET D 59 CG - SD - CE ANGL. DEV. = 11.0 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 LYS A 46 -123.98 57.49
REMARK 500 ASP A 61 -3.06 71.81
REMARK 500 TYR A 118 79.91 -158.61
REMARK 500 LYS B 46 -148.73 -134.62
REMARK 500 GLN B 47 127.52 -33.54
REMARK 500 GLN B 83 -5.56 74.03
REMARK 500 TYR B 118 79.22 -161.03
REMARK 500 ASP C 61 -3.90 72.62
REMARK 500 GLN C 83 -5.22 72.44
REMARK 500 TYR C 118 79.10 -156.35
REMARK 500 LYS D 46 -162.12 -103.75
REMARK 500 ASP D 61 -6.03 72.14
REMARK 500 TYR D 118 79.57 -159.79
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8YZ A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8YZ D 201
DBREF 5NIU A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
DBREF 5NIU B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
DBREF 5NIU C 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
DBREF 5NIU D 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
SEQADV 5NIU ALA A 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA A 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA A 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU LEU A 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU GLU A 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS A 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS A 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS A 142 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS A 143 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS A 144 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS A 145 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA B 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA B 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA B 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU LEU B 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU GLU B 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS B 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS B 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS B 142 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS B 143 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS B 144 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS B 145 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA C 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA C 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA C 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU LEU C 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU GLU C 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS C 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS C 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS C 142 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS C 143 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS C 144 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS C 145 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA D 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA D 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU ALA D 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU LEU D 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU GLU D 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS D 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS D 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS D 142 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS D 143 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS D 144 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5NIU HIS D 145 UNP Q9NZQ7 EXPRESSION TAG
SEQRES 1 A 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL
SEQRES 2 A 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO
SEQRES 3 A 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR
SEQRES 4 A 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS
SEQRES 5 A 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG
SEQRES 6 A 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY
SEQRES 7 A 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP
SEQRES 8 A 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA
SEQRES 9 A 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR
SEQRES 10 A 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
SEQRES 1 B 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL
SEQRES 2 B 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO
SEQRES 3 B 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR
SEQRES 4 B 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS
SEQRES 5 B 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG
SEQRES 6 B 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY
SEQRES 7 B 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP
SEQRES 8 B 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA
SEQRES 9 B 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR
SEQRES 10 B 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
SEQRES 1 C 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL
SEQRES 2 C 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO
SEQRES 3 C 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR
SEQRES 4 C 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS
SEQRES 5 C 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG
SEQRES 6 C 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY
SEQRES 7 C 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP
SEQRES 8 C 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA
SEQRES 9 C 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR
SEQRES 10 C 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
SEQRES 1 D 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL
SEQRES 2 D 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO
SEQRES 3 D 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR
SEQRES 4 D 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS
SEQRES 5 D 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG
SEQRES 6 D 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY
SEQRES 7 D 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP
SEQRES 8 D 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA
SEQRES 9 D 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR
SEQRES 10 D 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
HET 8YZ A 201 44
HET EDO A 202 4
HET EDO C 201 4
HET 8YZ D 201 44
HETNAM 8YZ (2~{R})-2-[[2-[(3-CYANOPHENYL)METHOXY]-4-[[3-(2,3-
HETNAM 2 8YZ DIHYDRO-1,4-BENZODIOXIN-6-YL)-2-METHYL-
HETNAM 3 8YZ PHENYL]METHOXY]-5-METHYL-PHENYL]METHYLAMINO]-3-
HETNAM 4 8YZ OXIDANYL-PROPANOIC ACID
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 5 8YZ 2(C35 H34 N2 O7)
FORMUL 6 EDO 2(C2 H6 O2)
FORMUL 9 HOH *318(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 LEU A 88 SER A 93 1 6
HELIX 4 AA4 LYS A 105 ALA A 109 5 5
HELIX 5 AA5 PRO A 133 HIS A 143 1 11
HELIX 6 AA6 ASP B 49 ALA B 52 5 4
HELIX 7 AA7 LEU B 74 GLN B 77 5 4
HELIX 8 AA8 HIS B 78 ARG B 82 5 5
HELIX 9 AA9 LEU B 88 SER B 93 1 6
HELIX 10 AB1 LYS B 105 ALA B 109 5 5
HELIX 11 AB2 PRO B 133 LEU B 138 1 6
HELIX 12 AB3 ASP C 49 ALA C 52 5 4
HELIX 13 AB4 LEU C 74 GLN C 77 5 4
HELIX 14 AB5 HIS C 78 ARG C 82 5 5
HELIX 15 AB6 LYS C 89 LEU C 94 5 6
HELIX 16 AB7 LYS C 105 ALA C 109 5 5
HELIX 17 AB8 PRO C 133 HIS C 141 1 9
HELIX 18 AB9 ASP D 49 ALA D 52 5 4
HELIX 19 AC1 LEU D 74 GLN D 77 5 4
HELIX 20 AC2 HIS D 78 ARG D 82 5 5
HELIX 21 AC3 LYS D 89 LEU D 94 5 6
HELIX 22 AC4 LYS D 105 ALA D 109 5 5
HELIX 23 AC5 PRO D 133 HIS D 144 1 12
SHEET 1 AA1 6 LEU A 27 GLU A 31 0
SHEET 2 AA1 6 ALA A 121 ASN A 131 1 O LYS A 129 N TYR A 28
SHEET 3 AA1 6 GLY A 110 SER A 117 -1 N TYR A 112 O ILE A 126
SHEET 4 AA1 6 ILE A 54 MET A 59 -1 N TYR A 56 O MET A 115
SHEET 5 AA1 6 LYS A 62 VAL A 68 -1 O PHE A 67 N VAL A 55
SHEET 6 AA1 6 GLU A 71 GLU A 72 -1 O GLU A 71 N VAL A 68
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 LYS B 129 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 ILE B 101 N MET B 36
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 ALA C 97 N CYS C 40
SHEET 3 AA6 3 ALA C 85 LEU C 87 -1 N ARG C 86 O GLN C 100
SHEET 1 AA7 6 LEU D 27 GLU D 31 0
SHEET 2 AA7 6 ALA D 121 ASN D 131 1 O LYS D 129 N TYR D 28
SHEET 3 AA7 6 GLY D 110 SER D 117 -1 N TYR D 112 O ILE D 126
SHEET 4 AA7 6 ILE D 54 MET D 59 -1 N TYR D 56 O MET D 115
SHEET 5 AA7 6 LYS D 62 VAL D 68 -1 O PHE D 67 N VAL D 55
SHEET 6 AA7 6 GLU D 71 GLU D 72 -1 O GLU D 71 N VAL D 68
SHEET 1 AA8 3 MET D 36 LYS D 41 0
SHEET 2 AA8 3 ASN D 96 ILE D 101 -1 O ALA D 97 N CYS D 40
SHEET 3 AA8 3 ALA D 85 LEU D 87 -1 N ARG D 86 O GLN D 100
SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.01
SSBOND 2 CYS B 40 CYS B 114 1555 1555 2.06
SSBOND 3 CYS C 40 CYS C 114 1555 1555 2.03
SSBOND 4 CYS D 40 CYS D 114 1555 1555 2.02
SITE 1 AC1 19 THR A 20 ILE A 54 TYR A 56 ALA A 121
SITE 2 AC1 19 ASP A 122 TYR A 123 LYS A 124 ARG A 125
SITE 3 AC1 19 EDO A 202 HOH A 327 HOH A 331 ILE B 54
SITE 4 AC1 19 TYR B 56 GLN B 66 VAL B 68 MET B 115
SITE 5 AC1 19 ALA B 121 ASP B 122 HOH B 225
SITE 1 AC2 6 TYR A 56 8YZ A 201 HOH A 306 ASP B 122
SITE 2 AC2 6 TYR B 123 HOH B 266
SITE 1 AC3 4 ASP C 122 HOH C 315 HOH C 324 8YZ D 201
SITE 1 AC4 16 ILE C 54 TYR C 56 ASP C 61 GLN C 66
SITE 2 AC4 16 VAL C 68 MET C 115 ASP C 122 EDO C 201
SITE 3 AC4 16 THR D 20 ILE D 54 TYR D 56 MET D 115
SITE 4 AC4 16 ALA D 121 ASP D 122 TYR D 123 LYS D 124
CRYST1 39.882 84.673 164.405 90.00 90.00 90.00 P 21 21 21 16
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 0.025074 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011810 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006083 0.00000