PDB Short entry for 4ZQK HEADER IMMUNE SYSTEM 10-MAY-15 4ZQK TITLE STRUCTURE OF THE COMPLEX OF HUMAN PROGRAMMED DEATH-1 (PD-1) AND ITS TITLE 2 LIGAND PD-L1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 33-150; COMPND 10 SYNONYM: HPD-1; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: 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 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: PDCD1, PD1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, CO-STIMULATION, RECEPTOR-LIGAND COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.M.ZAK,G.DUBIN,T.A.HOLAK REVDAT 4 10-JAN-24 4ZQK 1 REMARK REVDAT 3 16-DEC-15 4ZQK 1 JRNL REVDAT 2 09-DEC-15 4ZQK 1 JRNL REVDAT 1 04-NOV-15 4ZQK 0 JRNL AUTH K.M.ZAK,R.KITEL,S.PRZETOCKA,P.GOLIK,K.GUZIK,B.MUSIELAK, JRNL AUTH 2 A.DOMLING,G.DUBIN,T.A.HOLAK JRNL TITL STRUCTURE OF THE COMPLEX OF HUMAN PROGRAMMED DEATH 1, PD-1, JRNL TITL 2 AND ITS LIGAND PD-L1. JRNL REF STRUCTURE V. 23 2341 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 26602187 JRNL DOI 10.1016/J.STR.2015.09.010 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12082 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 625 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 863 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 2.33000 REMARK 3 B12 (A**2) : -0.36000 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): 0.286 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.234 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.316 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1684 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1535 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2296 ; 1.768 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3514 ; 0.860 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 7.670 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;34.544 ;24.925 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 254 ;17.366 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;12.728 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 271 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1926 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 373 ; 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): 881 ; 3.231 ; 4.015 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 880 ; 3.233 ; 4.015 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1096 ; 4.885 ; 6.011 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 18 A 132 REMARK 3 ORIGIN FOR THE GROUP (A): -9.7541 45.1745 114.2792 REMARK 3 T TENSOR REMARK 3 T11: 0.2385 T22: 0.0394 REMARK 3 T33: 0.0139 T12: -0.0829 REMARK 3 T13: -0.0151 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 3.1247 L22: 1.9953 REMARK 3 L33: 1.5961 L12: 1.1581 REMARK 3 L13: 0.4526 L23: -0.2608 REMARK 3 S TENSOR REMARK 3 S11: -0.1316 S12: 0.0009 S13: 0.0248 REMARK 3 S21: -0.1420 S22: 0.0472 S23: 0.0077 REMARK 3 S31: -0.0151 S32: -0.0567 S33: 0.0844 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 33 B 146 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8712 50.2693 104.1425 REMARK 3 T TENSOR REMARK 3 T11: 0.1611 T22: 0.2330 REMARK 3 T33: 0.0433 T12: 0.0465 REMARK 3 T13: -0.0563 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 2.3530 L22: 3.2100 REMARK 3 L33: 2.4375 L12: -0.1853 REMARK 3 L13: -0.7561 L23: 1.6745 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: 0.1309 S13: -0.1184 REMARK 3 S21: 0.2490 S22: 0.0563 S23: -0.1049 REMARK 3 S31: 0.3538 S32: 0.5131 S33: -0.0368 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 REMARK 4 REMARK 4 4ZQK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 5.5 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) : 0.91843 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12737 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 61.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.210 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: CHAIN A -3BIK, CHAIN B 3RRQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 1.84 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -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 38.12233 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 76.24467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.24467 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 38.12233 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: 1670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 ASP B 85 REMARK 465 ARG B 86 REMARK 465 SER B 87 REMARK 465 GLN B 88 REMARK 465 PRO B 89 REMARK 465 GLY B 90 REMARK 465 GLN B 91 REMARK 465 ASP B 92 REMARK 465 ARG B 147 REMARK 465 ARG B 148 REMARK 465 ALA B 149 REMARK 465 GLU B 150 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 LYS A 62 CD CE NZ REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 ASP A 73 CG OD1 OD2 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 OE1 NE2 REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 GLN A 107 CD OE1 NE2 REMARK 470 ARG A 125 NE CZ NH1 NH2 REMARK 470 LYS A 129 CD CE NZ REMARK 470 ASN B 33 CG OD1 ND2 REMARK 470 LEU B 41 CG CD1 CD2 REMARK 470 ASN B 58 CG OD1 ND2 REMARK 470 ARG B 69 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 96 CD NE CZ NH1 NH2 REMARK 470 ARG B 112 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 114 NE CZ NH1 NH2 REMARK 470 ARG B 115 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 131 CD CE NZ REMARK 470 LYS B 135 CE NZ REMARK 470 ARG B 139 CZ NH1 NH2 REMARK 470 ARG B 143 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 146 CG CD 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 SER B 71 O SER B 73 2.19 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 123 CA - CB - SG ANGL. DEV. = 7.5 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 GLU A 45 -120.30 -66.37 REMARK 500 TYR A 118 75.91 -175.40 REMARK 500 SER B 118 134.24 -38.33 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 NA A 201 DBREF 4ZQK A 18 132 UNP Q9NZQ7 PD1L1_HUMAN 18 132 DBREF 4ZQK B 33 150 UNP Q15116 PDCD1_HUMAN 33 150 SEQADV 4ZQK SER B 93 UNP Q15116 CYS 93 ENGINEERED MUTATION SEQRES 1 A 115 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 115 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 115 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 115 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 115 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 A 115 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 115 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 115 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 115 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA SEQRES 1 B 118 ASN PRO PRO THR PHE SER PRO ALA LEU LEU VAL VAL THR SEQRES 2 B 118 GLU GLY ASP ASN ALA THR PHE THR CYS SER PHE SER ASN SEQRES 3 B 118 THR SER GLU SER PHE VAL LEU ASN TRP TYR ARG MET SER SEQRES 4 B 118 PRO SER ASN GLN THR ASP LYS LEU ALA ALA PHE PRO GLU SEQRES 5 B 118 ASP ARG SER GLN PRO GLY GLN ASP SER ARG PHE ARG VAL SEQRES 6 B 118 THR GLN LEU PRO ASN GLY ARG ASP PHE HIS MET SER VAL SEQRES 7 B 118 VAL ARG ALA ARG ARG ASN ASP SER GLY THR TYR LEU CYS SEQRES 8 B 118 GLY ALA ILE SER LEU ALA PRO LYS ALA GLN ILE LYS GLU SEQRES 9 B 118 SER LEU ARG ALA GLU LEU ARG VAL THR GLU ARG ARG ALA SEQRES 10 B 118 GLU HET NA A 201 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *15(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 LYS A 89 LEU A 94 5 6 HELIX 5 AA5 LYS A 105 ALA A 109 5 5 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 GLY A 110 O VAL A 128 SHEET 4 AA1 6 ILE A 54 MET A 59 -1 N GLU A 58 O ARG A 113 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 4 THR B 36 SER B 38 0 SHEET 2 AA3 4 ALA B 50 SER B 55 -1 O THR B 53 N SER B 38 SHEET 3 AA3 4 ASP B 105 VAL B 110 -1 O VAL B 110 N ALA B 50 SHEET 4 AA3 4 PHE B 95 GLN B 99 -1 N ARG B 96 O SER B 109 SHEET 1 AA4 5 LEU B 41 THR B 45 0 SHEET 2 AA4 5 ALA B 140 THR B 145 1 O ARG B 143 N VAL B 44 SHEET 3 AA4 5 GLY B 119 ALA B 129 -1 N TYR B 121 O ALA B 140 SHEET 4 AA4 5 SER B 62 MET B 70 -1 N SER B 62 O LEU B 128 SHEET 5 AA4 5 THR B 76 PHE B 82 -1 O LEU B 79 N TRP B 67 SHEET 1 AA5 4 LEU B 41 THR B 45 0 SHEET 2 AA5 4 ALA B 140 THR B 145 1 O ARG B 143 N VAL B 44 SHEET 3 AA5 4 GLY B 119 ALA B 129 -1 N TYR B 121 O ALA B 140 SHEET 4 AA5 4 GLN B 133 GLU B 136 -1 O LYS B 135 N ALA B 125 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.08 SSBOND 2 CYS B 54 CYS B 123 1555 1555 2.13 CISPEP 1 GLY A 119 GLY A 120 0 0.04 CISPEP 2 SER B 38 PRO B 39 0 -7.36 CISPEP 3 PHE B 82 PRO B 83 0 -7.69 CISPEP 4 ALA B 129 PRO B 130 0 -3.96 SITE 1 AC1 2 ARG A 86 SER B 57 CRYST1 70.862 70.862 114.367 90.00 90.00 120.00 P 31 2 1 6 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 0.014112 0.008148 0.000000 0.00000 SCALE2 0.000000 0.016295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008744 0.00000