HEADER IMMUNE SYSTEM 08-AUG-22 8AOK TITLE COMPLEX OF PD-L1 WITH VHH6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A; 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; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: VHH 6; COMPND 9 CHAIN: B; COMPND 10 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; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: *; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 13 ORGANISM_TAXID: 9844; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: *; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET-21A(+) KEYWDS SINGLE DOMAIN ANTIBODY, VHH, PROGRAMMED CELL DEATH 1 LIGAND 1, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.KANG-PETTINGER,G.HALL REVDAT 2 07-FEB-24 8AOK 1 REMARK REVDAT 1 14-JUN-23 8AOK 0 JRNL AUTH T.KANG-PETTINGER,K.WALKER,R.BROWN,R.COWAN,H.WRIGHT, JRNL AUTH 2 R.BARAVALLE,L.C.WATERS,F.W.MUSKETT,M.W.BOWLER,K.SAWMYNADEN, JRNL AUTH 3 P.J.COOMBS,M.D.CARR,G.HALL JRNL TITL IDENTIFICATION, BINDING, AND STRUCTURAL CHARACTERIZATION OF JRNL TITL 2 SINGLE DOMAIN ANTI-PD-L1 ANTIBODIES INHIBITORY OF IMMUNE JRNL TITL 3 REGULATORY PROTEINS PD-1 AND CD80. JRNL REF J.BIOL.CHEM. V. 299 02769 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36470427 JRNL DOI 10.1016/J.JBC.2022.102769 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 56884 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) : 0.162 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.014 REMARK 3 FREE R VALUE TEST SET COUNT : 2852 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3910 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 240 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1903 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 311 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.43500 REMARK 3 B22 (A**2) : 0.43500 REMARK 3 B33 (A**2) : -0.87000 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): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2033 ; 0.018 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1899 ; 0.035 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2741 ; 2.138 ; 1.646 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4368 ; 2.391 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 7.017 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;28.654 ;21.909 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 335 ;13.431 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.376 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 253 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2410 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 494 ; 0.017 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 343 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 88 ; 0.321 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 949 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 221 ; 0.211 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.072 ; 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): 987 ; 2.482 ; 2.301 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 988 ; 2.481 ; 2.306 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1233 ; 3.342 ; 3.429 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1234 ; 3.347 ; 3.432 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1046 ; 3.957 ; 2.736 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1045 ; 3.958 ; 2.731 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1500 ; 5.586 ; 3.899 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1501 ; 5.585 ; 3.903 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 : 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 8AOK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1292124867. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965459 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56912 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 43.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.02200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 REMARK 200 STARTING MODEL: 3BIS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES:MOPS, PH 7.5, 0.02 M REMARK 280 AMMONIUM ACETATE, 0.02 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, REMARK 280 0.02 M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.02 M SODIUM FORMATE, REMARK 280 0.02M SODIUM OXAMATE, 10% (W/V) PEG 20000 AND 20% (V/V) PEG 500- REMARK 280 MME., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+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 49.78750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 49.78750 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.75750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.87875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.78750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 128.63625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.78750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 128.63625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.78750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.87875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 49.78750 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 49.78750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 85.75750 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 49.78750 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 49.78750 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 85.75750 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 49.78750 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 128.63625 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 49.78750 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 42.87875 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 49.78750 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 42.87875 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 49.78750 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 128.63625 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 49.78750 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 49.78750 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 85.75750 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 328 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 431 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 445 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 349 LIES ON A SPECIAL POSITION. 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 TYR A 134 REMARK 465 GLY B 0 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 H ASP A 49 HH TYR A 118 1.03 REMARK 500 HH TYR B 60 H ILE B 70 1.13 REMARK 500 HD1 HIS A 78 H SER A 80 1.22 REMARK 500 HE ARG B 19 O HOH B 303 1.52 REMARK 500 O HOH A 390 O HOH A 413 2.02 REMARK 500 O HOH B 303 O HOH B 431 2.10 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 O HOH A 422 O HOH A 434 15555 1.20 REMARK 500 H LEU A 48 OE1 GLN B 13 3545 1.55 REMARK 500 O HOH B 358 O HOH B 418 10555 2.06 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 GLU B 44 CD GLU B 44 OE2 0.103 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 A 40 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 CYS A 40 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 CYS A 114 CB - CA - C ANGL. DEV. = 11.0 DEGREES REMARK 500 CYS A 114 N - CA - CB ANGL. DEV. = -12.3 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 GLU A 47 127.34 -38.75 REMARK 500 ILE A 64 -64.04 -94.89 REMARK 500 ASP A 103 63.54 61.72 REMARK 500 TYR A 118 76.87 -157.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 97 10.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 451 DISTANCE = 6.14 ANGSTROMS DBREF 8AOK A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 8AOK B 0 127 PDB 8AOK 8AOK 0 127 SEQADV 8AOK GLU A 47 UNP Q9NZQ7 GLN 47 CONFLICT SEQRES 1 A 117 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 117 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 117 VAL GLU LYS GLU LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 117 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 117 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 A 117 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 117 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 117 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 117 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 1 B 128 GLY GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL SEQRES 2 B 128 GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 B 128 GLY ARG THR PHE SER ASN TYR HIS MET ALA TRP PHE ARG SEQRES 4 B 128 GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA GLY ILE SEQRES 5 B 128 SER TRP THR GLY ARG GLY THR TYR TYR THR ASP SER VAL SEQRES 6 B 128 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 128 THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 B 128 THR ALA VAL TYR TYR CYS ALA ALA GLU GLY THR LEU TYR SEQRES 9 B 128 GLY SER GLY GLY ARG THR HIS GLN SER ALA TYR ASP TYR SEQRES 10 B 128 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HET PEG A 201 17 HET ACY A 202 7 HET OXM A 203 8 HET PEG A 204 17 HET EDO A 205 10 HET EDO A 206 10 HET FMT A 207 5 HET PG4 B 201 31 HET PEG B 202 17 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ACY ACETIC ACID HETNAM OXM OXAMIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 PEG 3(C4 H10 O3) FORMUL 4 ACY C2 H4 O2 FORMUL 5 OXM C2 H3 N O3 FORMUL 7 EDO 2(C2 H6 O2) FORMUL 9 FMT C H2 O2 FORMUL 10 PG4 C8 H18 O5 FORMUL 12 HOH *311(H2 O) HELIX 1 AA1 HIS A 78 ARG A 82 5 5 HELIX 2 AA2 LEU A 88 SER A 93 1 6 HELIX 3 AA3 LYS A 105 ALA A 109 5 5 HELIX 4 AA4 ASP B 62 LYS B 65 5 4 HELIX 5 AA5 LYS B 87 THR B 91 5 5 HELIX 6 AA6 LEU B 102 GLY B 107 1 6 HELIX 7 AA7 HIS B 110 SER B 112 5 3 SHEET 1 AA1 6 LEU A 27 VAL A 30 0 SHEET 2 AA1 6 ALA A 121 VAL A 130 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 4 GLN B 3 SER B 7 0 SHEET 2 AA3 4 LEU B 18 SER B 25 -1 O SER B 21 N SER B 7 SHEET 3 AA3 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA3 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA4 6 LEU B 11 VAL B 12 0 SHEET 2 AA4 6 THR B 121 VAL B 125 1 O THR B 124 N VAL B 12 SHEET 3 AA4 6 ALA B 92 GLU B 99 -1 N TYR B 94 O THR B 121 SHEET 4 AA4 6 MET B 34 GLN B 39 -1 N ALA B 35 O ALA B 97 SHEET 5 AA4 6 GLU B 46 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 AA4 6 THR B 58 TYR B 60 -1 O TYR B 59 N GLY B 50 SHEET 1 AA5 4 LEU B 11 VAL B 12 0 SHEET 2 AA5 4 THR B 121 VAL B 125 1 O THR B 124 N VAL B 12 SHEET 3 AA5 4 ALA B 92 GLU B 99 -1 N TYR B 94 O THR B 121 SHEET 4 AA5 4 TYR B 114 TRP B 117 -1 O TYR B 116 N ALA B 98 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.22 CRYST1 99.575 99.575 171.515 90.00 90.00 90.00 I 41 2 2 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 0.010043 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005830 0.00000