HEADER IMMUNE SYSTEM 08-APR-16 5J8O
TITLE STRUCTURE OF HUMAN PROGRAMMED CELL DEATH 1 LIGAND 1 (PD-L1) WITH LOW
TITLE 2 MOLECULAR MASS INHIBITOR
CAVEAT 5J8O GLU A 60 HAS WRONG CHIRALITY AT ATOM CA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1;
COMPND 3 CHAIN: A, B;
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, PROGRAMMED CELL DEATH 1 LIGAND 1, CELL CYCLE, IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR K.M.ZAK,P.GRUDNIK,K.GUZIK,B.J.ZIEBA,B.MUSIELAK,P.DOEMLING,G.DUBIN,
AUTHOR 2 T.A.HOLAK
REVDAT 4 09-OCT-24 5J8O 1 REMARK
REVDAT 3 10-JAN-24 5J8O 1 REMARK
REVDAT 2 14-SEP-16 5J8O 1 JRNL
REVDAT 1 27-APR-16 5J8O 0
JRNL AUTH K.M.ZAK,P.GRUDNIK,K.GUZIK,B.J.ZIEBA,B.MUSIELAK,A.DOMLING,
JRNL AUTH 2 G.DUBIN,T.A.HOLAK
JRNL TITL STRUCTURAL BASIS FOR SMALL MOLECULE TARGETING OF THE
JRNL TITL 2 PROGRAMMED DEATH LIGAND 1 (PD-L1).
JRNL REF ONCOTARGET V. 7 30323 2016
JRNL REFN ESSN 1949-2553
JRNL PMID 27083005
JRNL DOI 10.18632/ONCOTARGET.8730
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0103
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.26
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 11974
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) : 0.245
REMARK 3 R VALUE (WORKING SET) : 0.241
REMARK 3 FREE R VALUE : 0.305
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 610
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 846
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89
REMARK 3 BIN R VALUE (WORKING SET) : 0.2670
REMARK 3 BIN FREE R VALUE SET COUNT : 32
REMARK 3 BIN FREE R VALUE : 0.4230
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1906
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 32
REMARK 3 SOLVENT ATOMS : 30
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.11
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.23000
REMARK 3 B22 (A**2) : 2.30000
REMARK 3 B33 (A**2) : -4.53000
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): 0.391
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.289
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.250
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.253
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1979 ; 0.014 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1870 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2689 ; 1.878 ; 1.975
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4280 ; 1.089 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 8.030 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;35.254 ;24.884
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 322 ;17.240 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;29.198 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 305 ; 0.214 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2240 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 447 ; 0.002 ; 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): 982 ; 3.302 ; 4.369
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 983 ; 3.301 ; 4.368
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1224 ; 4.759 ; 6.541
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 5J8O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-APR-16.
REMARK 100 THE DEPOSITION ID IS D_1000220140.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-AUG-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : BESSY
REMARK 200 BEAMLINE : 14.1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409
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 : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12626
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 47.260
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 6.800
REMARK 200 R MERGE (I) : 0.09300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.46500
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: PHASER 2.5.6, PHASER
REMARK 200 STARTING MODEL: 5C3T
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.22
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM FORMATE AND 20% (W/V)
REMARK 280 PEG 3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 X,-Y,-Z
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 -X,-Y+1/2,Z+1/2
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 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.59100
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.88650
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.59100
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 70.88650
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1270 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12610 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL
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 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 140
REMARK 465 HIS A 141
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 CB CG CD OE1 OE2
REMARK 470 GLN A 47 CG CD OE1 NE2
REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 129 CG CD CE NZ
REMARK 470 LYS B 46 CB CG CD CE NZ
REMARK 470 GLN B 47 CG CD OE1 NE2
REMARK 470 GLU B 71 CG CD OE1 OE2
REMARK 470 LYS B 75 CG CD CE NZ
REMARK 470 ARG B 82 CG CD NE CZ NH1 NH2
REMARK 470 ARG B 86 CG CD NE CZ NH1 NH2
REMARK 470 LEU B 88 CG CD1 CD2
REMARK 470 LYS B 89 CG CD CE NZ
REMARK 470 ASP B 90 CG OD1 OD2
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 302 O HOH B 216 2565 1.96
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 ARG B 84 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES
REMARK 500 ARG B 84 NE - CZ - NH2 ANGL. DEV. = 3.6 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 GLN A 47 127.99 -33.75
REMARK 500 MET A 59 -61.37 -106.51
REMARK 500 GLU A 60 -80.82 -74.41
REMARK 500 ASP A 61 -55.27 79.57
REMARK 500 TYR A 118 87.58 -160.94
REMARK 500 LEU A 138 127.09 -173.86
REMARK 500 GLU B 45 -126.35 -74.72
REMARK 500 HIS B 69 -126.95 59.67
REMARK 500 ASP B 90 -54.59 -28.45
REMARK 500 TYR B 118 89.74 -160.46
REMARK 500 LEU B 138 26.37 -71.23
REMARK 500 GLU B 139 -40.08 -27.39
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLU B 139 HIS B 140 -45.54
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 6GZ A 201
DBREF 5J8O A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
DBREF 5J8O B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134
SEQADV 5J8O ALA A 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O ALA A 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O ALA A 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O LEU A 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O GLU A 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O HIS A 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O HIS A 141 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O ALA B 135 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O ALA B 136 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O ALA B 137 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O LEU B 138 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O GLU B 139 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O HIS B 140 UNP Q9NZQ7 EXPRESSION TAG
SEQADV 5J8O HIS B 141 UNP Q9NZQ7 EXPRESSION TAG
SEQRES 1 A 124 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL
SEQRES 2 A 124 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO
SEQRES 3 A 124 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR
SEQRES 4 A 124 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS
SEQRES 5 A 124 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG
SEQRES 6 A 124 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY
SEQRES 7 A 124 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP
SEQRES 8 A 124 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA
SEQRES 9 A 124 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR
SEQRES 10 A 124 ALA ALA ALA LEU GLU HIS HIS
SEQRES 1 B 124 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL
SEQRES 2 B 124 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO
SEQRES 3 B 124 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR
SEQRES 4 B 124 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS
SEQRES 5 B 124 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG
SEQRES 6 B 124 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY
SEQRES 7 B 124 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP
SEQRES 8 B 124 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA
SEQRES 9 B 124 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR
SEQRES 10 B 124 ALA ALA ALA LEU GLU HIS HIS
HET 6GZ A 201 32
HETNAM 6GZ (2R)-1-({3-BROMO-4-[(2-METHYL[1,1'-BIPHENYL]-3-YL)
HETNAM 2 6GZ METHOXY]PHENYL}METHYL)PIPERIDINE-2-CARBOXYLIC ACID
FORMUL 3 6GZ C27 H28 BR N O3
FORMUL 4 HOH *30(H2 O)
HELIX 1 AA1 ASP A 49 ALA A 52 5 4
HELIX 2 AA2 LEU A 74 GLN A 77 5 4
HELIX 3 AA3 HIS A 78 ARG A 82 5 5
HELIX 4 AA4 LEU A 88 SER A 93 1 6
HELIX 5 AA5 LYS A 105 ALA A 109 5 5
HELIX 6 AA6 ASP B 49 LEU B 53 5 5
HELIX 7 AA7 HIS B 78 ARG B 82 5 5
HELIX 8 AA8 LYS B 89 GLY B 95 5 7
HELIX 9 AA9 LYS B 105 ALA B 109 5 5
HELIX 10 AB1 PRO B 133 LEU B 138 1 6
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 GLU A 58 -1 N TYR A 56 O MET A 115
SHEET 5 AA1 6 ASN A 63 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 ILE A 101 N MET A 36
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 ASN B 131 N VAL B 30
SHEET 3 AA3 6 GLY B 110 SER B 117 -1 N ILE B 116 O ASP B 122
SHEET 4 AA3 6 ILE B 54 MET B 59 -1 N GLU B 58 O ARG B 113
SHEET 5 AA3 6 LYS B 62 VAL B 68 -1 O ILE B 64 N TRP B 57
SHEET 6 AA3 6 GLU B 71 ASP B 73 -1 O ASP B 73 N GLN B 66
SHEET 1 AA4 3 MET B 36 ILE B 38 0
SHEET 2 AA4 3 LEU B 99 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
SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.02
SSBOND 2 CYS B 40 CYS B 114 1555 1555 2.07
CISPEP 1 GLU A 60 ASP A 61 0 -25.16
CISPEP 2 HIS B 140 HIS B 141 0 13.75
SITE 1 AC1 8 TYR A 56 GLN A 66 VAL A 76 MET A 115
SITE 2 AC1 8 TYR B 56 MET B 115 ALA B 121 ASP B 122
CRYST1 34.313 55.182 141.773 90.00 90.00 90.00 P 2 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 0.029143 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018122 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007054 0.00000