HEADER CELL CYCLE 05-FEB-20 6VQN TITLE CO-CRYSTAL STRUCTURE OF HUMAN PD-L1 COMPLEXED WITH COMPOUND A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: HPD-L1,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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS COMPLEX, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR A.WHITE,D.LAKSHMINARASIMHAN,C.LEO,R.K.SUTO REVDAT 4 16-OCT-24 6VQN 1 REMARK REVDAT 3 11-OCT-23 6VQN 1 REMARK REVDAT 2 10-MAR-21 6VQN 1 JRNL REVDAT 1 20-JAN-21 6VQN 0 JRNL AUTH J.J.PARK,E.P.THI,V.H.CARPIO,Y.BI,A.G.COLE,B.D.DORSEY,K.FAN, JRNL AUTH 2 T.HARASYM,C.L.IOTT,S.KADHIM,J.H.KIM,A.C.H.LEE,D.NGUYEN, JRNL AUTH 3 B.S.PARATALA,R.QIU,A.WHITE,D.LAKSHMINARASIMHAN,C.LEO, JRNL AUTH 4 R.K.SUTO,R.RIJNBRAND,S.TANG,M.J.SOFIA,C.B.MOORE JRNL TITL CHECKPOINT INHIBITION THROUGH SMALL MOLECULE-INDUCED JRNL TITL 2 INTERNALIZATION OF PROGRAMMED DEATH-LIGAND 1. JRNL REF NAT COMMUN V. 12 1222 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33619272 JRNL DOI 10.1038/S41467-021-21410-1 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 23114 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1117 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1703 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.24000 REMARK 3 B22 (A**2) : -1.87000 REMARK 3 B33 (A**2) : 5.12000 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): 0.243 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.357 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3037 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2838 ; 0.004 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4107 ; 1.663 ; 1.667 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6566 ; 1.378 ; 1.603 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 6.585 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;35.916 ;23.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 529 ;20.813 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;27.130 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 383 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3353 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 623 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 6VQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97928 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24239 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 80.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 1.16300 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: MOLREP REMARK 200 STARTING MODEL: 4ZQK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NACITRATE, PH 6.5 AND 22% (W/V) REMARK 280 PEG 3000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 40.29250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.29250 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 49.50150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 86.08650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.50150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 86.08650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.29250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.50150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 86.08650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.29250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.50150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 86.08650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 17 REMARK 465 GLU A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 REMARK 465 MET B 17 REMARK 465 ALA B 137 REMARK 465 LEU B 138 REMARK 465 GLU 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 HIS B 145 REMARK 465 MET C 17 REMARK 465 HIS C 143 REMARK 465 HIS C 144 REMARK 465 HIS C 145 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 LEU A 138 CG CD1 CD2 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 NH2 ARG A 86 OD2 ASP C 103 8545 2.07 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 LYS A 46 -138.91 63.09 REMARK 500 TYR A 118 90.26 -160.88 REMARK 500 LYS B 46 -121.35 62.01 REMARK 500 ASP B 103 65.28 62.23 REMARK 500 TYR B 118 87.18 -158.65 REMARK 500 LYS C 46 -119.91 51.65 REMARK 500 ASP C 61 -2.48 80.14 REMARK 500 HIS C 140 -51.04 -122.94 REMARK 500 HIS C 141 82.43 -69.98 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 241 DISTANCE = 5.82 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R81 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R81 C 201 DBREF 6VQN A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 6VQN B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 6VQN C 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 SEQADV 6VQN MET A 17 UNP Q9NZQ7 INITIATING METHIONINE SEQADV 6VQN ALA A 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN ALA A 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN ALA A 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN LEU A 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN GLU A 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS A 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS A 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS A 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS A 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS A 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS A 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN MET B 17 UNP Q9NZQ7 INITIATING METHIONINE SEQADV 6VQN ALA B 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN ALA B 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN ALA B 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN LEU B 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN GLU B 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS B 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS B 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS B 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS B 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS B 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS B 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN MET C 17 UNP Q9NZQ7 INITIATING METHIONINE SEQADV 6VQN ALA C 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN ALA C 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN ALA C 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN LEU C 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN GLU C 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS C 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS C 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS C 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS C 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS C 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6VQN HIS C 145 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 129 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL SEQRES 2 A 129 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE SEQRES 3 A 129 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL SEQRES 4 A 129 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL SEQRES 5 A 129 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR SEQRES 6 A 129 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU SEQRES 7 A 129 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN SEQRES 8 A 129 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY SEQRES 9 A 129 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO SEQRES 10 A 129 TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 129 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL SEQRES 2 B 129 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE SEQRES 3 B 129 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL SEQRES 4 B 129 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL SEQRES 5 B 129 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR SEQRES 6 B 129 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU SEQRES 7 B 129 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN SEQRES 8 B 129 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY SEQRES 9 B 129 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO SEQRES 10 B 129 TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 129 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL SEQRES 2 C 129 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE SEQRES 3 C 129 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL SEQRES 4 C 129 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL SEQRES 5 C 129 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR SEQRES 6 C 129 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU SEQRES 7 C 129 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN SEQRES 8 C 129 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY SEQRES 9 C 129 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO SEQRES 10 C 129 TYR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET R81 B 201 42 HET R81 C 201 21 HETNAM R81 N,N'-(2,2'-DIMETHYL[1,1'-BIPHENYL]-3,3'-DIYL)BIS(5- HETNAM 2 R81 {[(2-HYDROXYETHYL)AMINO]METHYL}PYRIDINE-2-CARBOXAMIDE) FORMUL 4 R81 2(C32 H36 N6 O4) FORMUL 6 HOH *139(H2 O) HELIX 1 AA1 ASP A 49 ALA A 52 5 4 HELIX 2 AA2 HIS A 78 ARG A 82 5 5 HELIX 3 AA3 LYS A 89 LEU A 94 5 6 HELIX 4 AA4 LYS A 105 ALA A 109 5 5 HELIX 5 AA5 ASP B 49 ALA B 52 5 4 HELIX 6 AA6 LEU B 74 GLN B 77 5 4 HELIX 7 AA7 HIS B 78 ARG B 82 5 5 HELIX 8 AA8 GLN B 91 LEU B 94 5 4 HELIX 9 AA9 LYS B 105 ALA B 109 5 5 HELIX 10 AB1 ASP C 49 ALA C 52 5 4 HELIX 11 AB2 HIS C 78 ARG C 82 5 5 HELIX 12 AB3 GLN C 91 LEU C 94 5 4 HELIX 13 AB4 LYS C 105 ALA C 109 5 5 SHEET 1 AA1 5 LEU A 27 GLU A 31 0 SHEET 2 AA1 5 ALA A 121 ASN A 131 1 O LYS A 129 N VAL A 30 SHEET 3 AA1 5 GLY A 110 SER A 117 -1 N TYR A 112 O ILE A 126 SHEET 4 AA1 5 ILE A 54 MET A 59 -1 N TYR A 56 O MET A 115 SHEET 5 AA1 5 LYS A 62 VAL A 68 -1 O PHE A 67 N VAL A 55 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 6 LEU B 27 GLU B 31 0 SHEET 2 AA3 6 ALA B 121 ASN B 131 1 O THR B 127 N TYR B 28 SHEET 3 AA3 6 GLY B 110 SER B 117 -1 N TYR B 112 O ILE B 126 SHEET 4 AA3 6 ILE B 54 MET B 59 -1 N TYR B 56 O MET B 115 SHEET 5 AA3 6 LYS B 62 VAL B 68 -1 O PHE B 67 N VAL B 55 SHEET 6 AA3 6 GLU B 71 GLU B 72 -1 O GLU B 71 N VAL B 68 SHEET 1 AA4 3 MET B 36 LYS B 41 0 SHEET 2 AA4 3 ASN B 96 ILE B 101 -1 O ALA B 97 N CYS B 40 SHEET 3 AA4 3 ALA B 85 LEU B 87 -1 N ARG B 86 O GLN B 100 SHEET 1 AA5 6 LEU C 27 GLU C 31 0 SHEET 2 AA5 6 ALA C 121 ASN C 131 1 O LYS C 129 N TYR C 28 SHEET 3 AA5 6 GLY C 110 SER C 117 -1 N TYR C 112 O ILE C 126 SHEET 4 AA5 6 ILE C 54 MET C 59 -1 N TYR C 56 O MET C 115 SHEET 5 AA5 6 LYS C 62 VAL C 68 -1 O PHE C 67 N VAL C 55 SHEET 6 AA5 6 GLU C 71 GLU C 72 -1 O GLU C 71 N VAL C 68 SHEET 1 AA6 3 MET C 36 LYS C 41 0 SHEET 2 AA6 3 ASN C 96 ILE C 101 -1 O ILE C 101 N MET C 36 SHEET 3 AA6 3 ALA C 85 LEU C 87 -1 N ARG C 86 O GLN C 100 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.01 SSBOND 2 CYS B 40 CYS B 114 1555 1555 2.00 SSBOND 3 CYS C 40 CYS C 114 1555 1555 2.01 LINK C R81 C 201 C R81 C 201 1555 4555 1.45 SITE 1 AC1 19 TYR A 56 MET A 115 ILE A 116 SER A 117 SITE 2 AC1 19 ALA A 121 ASP A 122 TYR A 123 TYR B 56 SITE 3 AC1 19 GLN B 66 MET B 115 ILE B 116 SER B 117 SITE 4 AC1 19 ALA B 121 ASP B 122 TYR B 123 LYS B 124 SITE 5 AC1 19 HOH B 314 HOH B 315 HOH B 317 SITE 1 AC2 11 VAL C 21 TYR C 56 MET C 115 ILE C 116 SITE 2 AC2 11 SER C 117 ALA C 121 ASP C 122 TYR C 123 SITE 3 AC2 11 HOH C 305 HOH C 318 HOH C 324 CRYST1 99.003 172.173 80.585 90.00 90.00 90.00 C 2 2 21 24 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 0.010101 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005808 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012409 0.00000