HEADER IMMUNE SYSTEM 17-APR-16 5JDS TITLE CRYSTAL STRUCTURE OF PD-L1 COMPLEXED WITH A NANOBODY AT 1.7 ANGSTRON TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: UNP RESIDUES 18-132; COMPND 9 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELIDAE; SOURCE 3 ORGANISM_TAXID: 9835; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.ZHOU,H.WEI REVDAT 2 09-OCT-24 5JDS 1 REMARK REVDAT 1 12-APR-17 5JDS 0 JRNL AUTH F.ZHANG,H.WEI,X.WANG,Y.BAI,P.WANG,J.WU,X.JIANG,Y.WANG,H.CAI, JRNL AUTH 2 T.XU,A.ZHOU JRNL TITL STRUCTURAL BASIS OF A NOVEL PD-L1 NANOBODY FOR IMMUNE JRNL TITL 2 CHECKPOINT BLOCKADE. JRNL REF CELL DISCOV V. 3 17004 2017 JRNL REFN ESSN 2056-5968 JRNL PMID 28280600 JRNL DOI 10.1038/CELLDISC.2017.4 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29996 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1611 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2193 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1879 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.17000 REMARK 3 B12 (A**2) : 0.05000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.657 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1930 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1836 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2617 ; 1.455 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4218 ; 0.718 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 6.740 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;33.408 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 342 ;13.237 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;17.879 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 293 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2194 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 442 ; 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): 972 ; 1.210 ; 1.667 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 971 ; 1.210 ; 1.665 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1213 ; 2.024 ; 2.491 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1214 ; 2.023 ; 2.492 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 958 ; 1.680 ; 1.904 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 955 ; 1.668 ; 1.896 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1392 ; 2.679 ; 2.753 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2116 ; 5.439 ;13.938 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2075 ; 5.325 ;13.647 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 : B 1 B 127 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1969 -47.0791 -12.5326 REMARK 3 T TENSOR REMARK 3 T11: 0.0526 T22: 0.0451 REMARK 3 T33: 0.0288 T12: 0.0000 REMARK 3 T13: 0.0001 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.8752 L22: 1.6173 REMARK 3 L33: 1.8728 L12: -0.3223 REMARK 3 L13: -0.4066 L23: 1.4231 REMARK 3 S TENSOR REMARK 3 S11: -0.0554 S12: -0.1457 S13: 0.0822 REMARK 3 S21: 0.1195 S22: 0.0468 S23: 0.0171 REMARK 3 S31: 0.0853 S32: -0.0291 S33: 0.0087 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 : A 18 A 132 REMARK 3 ORIGIN FOR THE GROUP (A): 23.6916 -52.5211 -37.5199 REMARK 3 T TENSOR REMARK 3 T11: 0.0440 T22: 0.0566 REMARK 3 T33: 0.0462 T12: -0.0267 REMARK 3 T13: -0.0072 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 1.2046 L22: 1.4572 REMARK 3 L33: 0.8358 L12: -0.0872 REMARK 3 L13: -0.3271 L23: -0.2923 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: 0.1741 S13: -0.0646 REMARK 3 S21: -0.1522 S22: -0.0260 S23: -0.0371 REMARK 3 S31: 0.0541 S32: -0.0288 S33: 0.0577 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 5JDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220303. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9777 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31640 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 51.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 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) : NULL 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: NULL 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 (%): 49.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M NACL, 1.4M (NH4)2SO4, LIQUID REMARK 280 DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 24.41000 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 48.82000 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 36.61500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.02500 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 12.20500 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: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A 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 THR B -1 REMARK 465 GLY B 0 REMARK 465 SER B 128 REMARK 465 GLY B 129 REMARK 465 SER B 130 REMARK 465 MET B 131 REMARK 465 ASP B 132 REMARK 465 PRO B 133 REMARK 465 GLY B 134 REMARK 465 GLY B 135 REMARK 465 SER B 136 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS 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 MET A 17 REMARK 465 LEU A 133 REMARK 465 GLU A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 REMARK 465 HIS A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 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 OG SER B 111 O HOH B 301 2.16 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 CL CL B 203 O HOH A 305 6445 2.04 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 A 113 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -5.5 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 ALA B 92 165.63 179.87 REMARK 500 GLU A 60 -112.35 52.53 REMARK 500 TYR A 118 69.83 -163.49 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 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 DBREF 5JDS B -1 144 PDB 5JDS 5JDS -1 144 DBREF 5JDS A 18 132 UNP Q9NZQ7 PD1L1_HUMAN 18 132 SEQADV 5JDS MET A 17 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS LEU A 133 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS GLU A 134 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS HIS A 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS HIS A 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS HIS A 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS HIS A 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS HIS A 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDS HIS A 140 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 B 146 THR GLY GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU SEQRES 2 B 146 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 B 146 SER GLY LYS MET SER SER ARG ARG CYS MET ALA TRP PHE SEQRES 4 B 146 ARG GLN ALA PRO GLY LYS GLU ARG GLU ARG VAL ALA LYS SEQRES 5 B 146 LEU LEU THR THR SER GLY SER THR TYR LEU ALA ASP SER SEQRES 6 B 146 VAL LYS GLY ARG PHE THR ILE SER GLN ASN ASN ALA LYS SEQRES 7 B 146 SER THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 8 B 146 ASP THR ALA MET TYR TYR CYS ALA ALA ASP SER PHE GLU SEQRES 9 B 146 ASP PRO THR CYS THR LEU VAL THR SER SER GLY ALA PHE SEQRES 10 B 146 GLN TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 11 B 146 GLY SER MET ASP PRO GLY GLY SER HIS HIS HIS HIS HIS SEQRES 12 B 146 HIS HIS HIS SEQRES 1 A 124 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL SEQRES 2 A 124 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE SEQRES 3 A 124 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL SEQRES 4 A 124 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL SEQRES 5 A 124 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR SEQRES 6 A 124 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU SEQRES 7 A 124 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN SEQRES 8 A 124 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY SEQRES 9 A 124 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA LEU SEQRES 10 A 124 GLU HIS HIS HIS HIS HIS HIS HET NA B 201 1 HET CL B 202 1 HET CL B 203 1 HET CL B 204 1 HET SO4 A 201 5 HET NA A 202 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 3 NA 2(NA 1+) FORMUL 4 CL 3(CL 1-) FORMUL 7 SO4 O4 S 2- FORMUL 9 HOH *159(H2 O) HELIX 1 AA1 LYS B 27 ARG B 31 5 5 HELIX 2 AA2 LYS B 87 THR B 91 5 5 HELIX 3 AA3 PRO B 104 VAL B 109 1 6 HELIX 4 AA4 SER B 111 PHE B 115 5 5 HELIX 5 AA5 LYS A 89 LEU A 94 5 6 HELIX 6 AA6 LYS A 105 ALA A 109 5 5 SHEET 1 AA1 4 GLN B 3 SER B 7 0 SHEET 2 AA1 4 LEU B 18 SER B 25 -1 O ALA B 23 N GLN B 5 SHEET 3 AA1 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA1 4 PHE B 68 GLN B 72 -1 N SER B 71 O TYR B 80 SHEET 1 AA2 6 GLY B 10 VAL B 12 0 SHEET 2 AA2 6 THR B 122 VAL B 126 1 O THR B 125 N GLY B 10 SHEET 3 AA2 6 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 122 SHEET 4 AA2 6 CYS B 33 GLN B 39 -1 N PHE B 37 O TYR B 95 SHEET 5 AA2 6 GLU B 46 LEU B 52 -1 O VAL B 48 N TRP B 36 SHEET 6 AA2 6 THR B 58 LEU B 60 -1 O TYR B 59 N LYS B 50 SHEET 1 AA3 4 GLY B 10 VAL B 12 0 SHEET 2 AA3 4 THR B 122 VAL B 126 1 O THR B 125 N GLY B 10 SHEET 3 AA3 4 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 122 SHEET 4 AA3 4 TYR B 117 TRP B 118 -1 O TYR B 117 N ALA B 98 SHEET 1 AA4 6 LEU A 27 GLU A 31 0 SHEET 2 AA4 6 ALA A 121 ASN A 131 1 O LYS A 129 N VAL A 30 SHEET 3 AA4 6 GLY A 110 SER A 117 -1 N TYR A 112 O ILE A 126 SHEET 4 AA4 6 ILE A 54 MET A 59 -1 N TYR A 56 O MET A 115 SHEET 5 AA4 6 LYS A 62 VAL A 68 -1 O ILE A 64 N TRP A 57 SHEET 6 AA4 6 GLU A 71 GLU A 72 -1 O GLU A 71 N VAL A 68 SHEET 1 AA5 3 MET A 36 LYS A 41 0 SHEET 2 AA5 3 ASN A 96 ILE A 101 -1 O ALA A 97 N CYS A 40 SHEET 3 AA5 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100 SSBOND 1 CYS B 22 CYS B 96 1555 1555 2.08 SSBOND 2 CYS B 33 CYS B 106 1555 1555 2.03 SSBOND 3 CYS A 40 CYS A 114 1555 1555 2.01 LINK NA NA B 201 O HOH B 367 1555 1555 3.03 CISPEP 1 ASP B 103 PRO B 104 0 -0.67 SITE 1 AC1 3 ASN B 74 CL B 204 HOH B 367 SITE 1 AC2 3 LYS A 46 TYR B 59 ASP B 62 SITE 1 AC3 2 HOH A 305 ARG B 47 SITE 1 AC4 2 ASN B 74 NA B 201 SITE 1 AC5 3 TYR A 123 ARG A 125 GLN B 116 SITE 1 AC6 1 LEU A 48 CRYST1 83.130 83.130 73.230 90.00 90.00 120.00 P 61 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 0.012029 0.006945 0.000000 0.00000 SCALE2 0.000000 0.013890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013656 0.00000