HEADER ANTITUMOR PROTEIN 25-MAY-23 8P64 TITLE CO-CRYSTAL STRUCTURE OF PD-L1 WITH LOW MOLECULAR WEIGHT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PD-L1,PDCD1 LIGAND 1,PROGRAMMED DEATH LIGAND 1,HPD-L1,B7 COMPND 5 HOMOLOG 1,B7-H1; COMPND 6 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 KEYWDS PD-L1, INHIBITOR COMPLEX, ANTITUMOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.PLEWKA,K.MAGIERA-MULARZ,R.VAN DER STRAAT,R.DRAIJER,E.SURMIAK, AUTHOR 2 R.BUTERA,L.LAND,B.MUSIELAK,A.DOMLING REVDAT 2 15-MAY-24 8P64 1 JRNL REVDAT 1 06-MAR-24 8P64 0 JRNL AUTH R.VAN DER STRAAT,R.DRAIJER,E.SURMIAK,R.BUTERA,L.LAND, JRNL AUTH 2 K.MAGIERA-MULARZ,B.MUSIELAK,J.PLEWKA,T.A.HOLAK,A.DOMLING JRNL TITL 1,5-DISUBSTITUTED TETRAZOLES AS PD-1/PD-L1 ANTAGONISTS. JRNL REF RSC MED CHEM V. 15 1210 2024 JRNL REFN ESSN 2632-8682 JRNL PMID 38665826 JRNL DOI 10.1039/D3MD00746D REMARK 2 REMARK 2 RESOLUTION. 3.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0411 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) : 3.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.723 REMARK 3 FREE R VALUE TEST SET COUNT : 224 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) : 3.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 329 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3740 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1765 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 97.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05200 REMARK 3 B22 (A**2) : -0.05200 REMARK 3 B33 (A**2) : 0.16900 REMARK 3 B12 (A**2) : -0.02600 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.631 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.603 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.532 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1822 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1684 ; 0.004 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2482 ; 1.744 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3827 ; 0.803 ; 1.564 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 233 ; 8.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 12 ;16.027 ; 7.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 273 ;18.785 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 288 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2160 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 419 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 276 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 31 ; 0.323 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 872 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 48 ; 0.308 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.036 ; 0.200 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): 938 ; 6.951 ;10.710 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 938 ; 6.951 ;10.710 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1169 ;11.053 ;19.236 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1170 ;11.049 ;19.242 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 884 ; 6.747 ;10.916 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 885 ; 6.745 ;10.916 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1313 ;10.814 ;20.002 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1314 ;10.810 ;20.001 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 4 A 119 NULL REMARK 3 1 A 4 A 119 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8P64 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-23 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 : 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) : 0.9184 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 : 4743 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.310 REMARK 200 RESOLUTION RANGE LOW (A) : 48.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.55 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.51 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.960 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 (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M S38 SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE 0.01 M SODIUM BORATE, PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K 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 32.02667 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 64.05333 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 64.05333 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 32.02667 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 ALA A 121 REMARK 465 ALA A 122 REMARK 465 ALA A 123 REMARK 465 LEU A 124 REMARK 465 GLU A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 ALA B 122 REMARK 465 ALA B 123 REMARK 465 LEU B 124 REMARK 465 GLU B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 465 HIS B 131 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 LYS A 11 CG CD CE NZ REMARK 470 GLU A 31 CB CG CD OE1 OE2 REMARK 470 LYS A 32 CB CG CD CE NZ REMARK 470 GLN A 33 CG CD OE1 NE2 REMARK 470 LEU A 34 CG CD1 CD2 REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLN A 52 CG CD OE1 NE2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 GLN A 63 CG CD OE1 NE2 REMARK 470 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 TYR A 120 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE B 5 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 GLU B 17 CG CD OE1 OE2 REMARK 470 GLU B 31 CB CG CD OE1 OE2 REMARK 470 LYS B 32 CB CG CD CE NZ REMARK 470 GLN B 33 CG CD OE1 NE2 REMARK 470 GLU B 46 CG CD OE1 OE2 REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 LYS B 91 CG CD CE NZ REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 TYR B 120 CG CD1 CD2 CE1 CE2 CZ OH 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 HG CYS B 26 SG CYS B 100 1.09 REMARK 500 HG CYS A 26 SG CYS A 100 1.22 REMARK 500 H LEU A 85 O HOH A 201 1.26 REMARK 500 SG CYS A 26 HG CYS A 100 1.47 REMARK 500 SG CYS B 26 HG CYS B 100 1.53 REMARK 500 O ILE A 24 O HOH A 201 1.90 REMARK 500 N LEU A 85 O HOH A 201 2.15 REMARK 500 OD1 ASP A 76 O HOH A 202 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 HB3 TYR A 120 O HOH B 306 3664 1.51 REMARK 500 O ALA A 118 H LEU B 36 6664 1.58 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 HIS A 55 CB - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 ARG A 99 CG - CD - NE ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG B 68 CB - CG - CD ANGL. DEV. = 16.3 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 33 -69.66 -109.31 REMARK 500 LEU A 34 65.48 62.90 REMARK 500 ASP A 89 76.88 51.75 REMARK 500 TYR A 104 83.34 -158.55 REMARK 500 PHE B 5 -129.45 49.29 REMARK 500 VAL B 30 -83.81 -105.14 REMARK 500 GLU B 31 74.85 91.69 REMARK 500 LYS B 32 -125.06 106.56 REMARK 500 ARG B 70 -54.23 -134.83 REMARK 500 TYR B 104 75.13 -153.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 70 0.14 SIDE CHAIN REMARK 500 ARG B 68 0.09 SIDE CHAIN REMARK 500 ARG B 70 0.14 SIDE CHAIN REMARK 500 ARG B 72 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8P64 A 4 120 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 8P64 B 4 120 UNP Q9NZQ7 PD1L1_HUMAN 18 134 SEQADV 8P64 MET A 1 UNP Q9NZQ7 INITIATING METHIONINE SEQADV 8P64 GLY A 2 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 SER A 3 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 ALA A 121 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 ALA A 122 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 ALA A 123 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 LEU A 124 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 GLU A 125 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS A 126 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS A 127 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS A 128 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS A 129 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS A 130 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS A 131 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 MET B 1 UNP Q9NZQ7 INITIATING METHIONINE SEQADV 8P64 GLY B 2 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 SER B 3 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 ALA B 121 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 ALA B 122 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 ALA B 123 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 LEU B 124 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 GLU B 125 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS B 126 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS B 127 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS B 128 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS B 129 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS B 130 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8P64 HIS B 131 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 131 MET GLY SER ALA PHE THR VAL THR VAL PRO LYS ASP LEU SEQRES 2 A 131 TYR VAL VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS SEQRES 3 A 131 LYS PHE PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU SEQRES 4 A 131 ILE VAL TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN SEQRES 5 A 131 PHE VAL HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SEQRES 6 A 131 SER TYR ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SEQRES 7 A 131 SER LEU GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS SEQRES 8 A 131 LEU GLN ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR SEQRES 9 A 131 GLY GLY ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN SEQRES 10 A 131 ALA PRO TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS SEQRES 11 A 131 HIS SEQRES 1 B 131 MET GLY SER ALA PHE THR VAL THR VAL PRO LYS ASP LEU SEQRES 2 B 131 TYR VAL VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS SEQRES 3 B 131 LYS PHE PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU SEQRES 4 B 131 ILE VAL TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN SEQRES 5 B 131 PHE VAL HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SEQRES 6 B 131 SER TYR ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SEQRES 7 B 131 SER LEU GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS SEQRES 8 B 131 LEU GLN ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR SEQRES 9 B 131 GLY GLY ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN SEQRES 10 B 131 ALA PRO TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS SEQRES 11 B 131 HIS HET X1Q B 201 45 HETNAM X1Q ~{N}-[[1-[(~{E})-2-(2-METHYL-3-PHENYL-PHENYL)ETHENYL]- HETNAM 2 X1Q 1,2,3,4-TETRAZOL-5-YL]METHYL]ETHANAMINE FORMUL 3 X1Q C19 H21 N5 FORMUL 4 HOH *10(H2 O) HELIX 1 AA1 HIS A 64 ARG A 68 5 5 HELIX 2 AA2 LYS A 75 SER A 79 1 5 HELIX 3 AA3 LYS A 91 ALA A 95 5 5 HELIX 4 AA4 ASP B 35 ALA B 37 5 3 HELIX 5 AA5 ASP B 59 GLN B 63 5 5 HELIX 6 AA6 HIS B 64 ARG B 68 5 5 HELIX 7 AA7 LEU B 74 SER B 79 1 6 HELIX 8 AA8 LYS B 91 ALA B 95 5 5 SHEET 1 AA1 6 LEU A 13 GLU A 17 0 SHEET 2 AA1 6 ALA A 107 ASN A 117 1 O ASN A 117 N VAL A 16 SHEET 3 AA1 6 GLY A 96 SER A 103 -1 N TYR A 98 O ILE A 112 SHEET 4 AA1 6 ILE A 40 MET A 45 -1 N TYR A 42 O MET A 101 SHEET 5 AA1 6 LYS A 48 VAL A 54 -1 O PHE A 53 N VAL A 41 SHEET 6 AA1 6 GLU A 57 GLU A 58 -1 O GLU A 57 N VAL A 54 SHEET 1 AA2 3 MET A 22 LYS A 27 0 SHEET 2 AA2 3 ASN A 82 ILE A 87 -1 O ALA A 83 N CYS A 26 SHEET 3 AA2 3 ALA A 71 LEU A 74 -1 N ARG A 72 O GLN A 86 SHEET 1 AA3 5 LEU B 13 GLU B 17 0 SHEET 2 AA3 5 ALA B 107 ASN B 117 1 O ASN B 117 N VAL B 16 SHEET 3 AA3 5 GLY B 96 TYR B 104 -1 N TYR B 98 O ILE B 112 SHEET 4 AA3 5 LEU B 39 MET B 45 -1 N TYR B 42 O MET B 101 SHEET 5 AA3 5 LYS B 48 VAL B 54 -1 O PHE B 53 N VAL B 41 SHEET 1 AA4 3 MET B 22 LYS B 27 0 SHEET 2 AA4 3 ASN B 82 ILE B 87 -1 O ALA B 83 N CYS B 26 SHEET 3 AA4 3 ALA B 71 LEU B 73 -1 N ARG B 72 O GLN B 86 SSBOND 1 CYS A 26 CYS A 100 1555 1555 2.31 SSBOND 2 CYS B 26 CYS B 100 1555 1555 2.28 CRYST1 73.450 73.450 96.080 90.00 90.00 120.00 P 31 2 1 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 0.013615 0.007860 0.000000 0.00000 SCALE2 0.000000 0.015721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010408 0.00000