HEADER IMMUNE SYSTEM 20-MAR-19 6R3K TITLE STRUCTURE OF HUMAN PROGRAMMED CELL DEATH 1 LIGAND 1 (PD-L1) WITH LOW TITLE 2 MOLECULAR MASS INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PROGRAMMED DEATH LIGAND 1,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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PD-L1, PD-1, IMMUNE CHECKPOINT, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.M.ZAK,P.GRUDNIK,L.SKALNIAK,G.DUBIN,T.A.HOLAK REVDAT 4 24-JAN-24 6R3K 1 REMARK REVDAT 3 25-AUG-21 6R3K 1 JRNL REVDAT 2 08-MAY-19 6R3K 1 REMARK LINK REVDAT 1 03-APR-19 6R3K 0 SPRSDE 03-APR-19 6R3K 5NIX JRNL AUTH D.MUSZAK,E.SURMIAK,J.PLEWKA,K.MAGIERA-MULARZ,J.KOCIK-KROL, JRNL AUTH 2 B.MUSIELAK,D.SALA,R.KITEL,M.STEC,K.WEGLARCZYK,M.SIEDLAR, JRNL AUTH 3 A.DOMLING,L.SKALNIAK,T.A.HOLAK JRNL TITL TERPHENYL-BASED SMALL-MOLECULE INHIBITORS OF PROGRAMMED CELL JRNL TITL 2 DEATH-1/PROGRAMMED DEATH-LIGAND 1 PROTEIN-PROTEIN JRNL TITL 3 INTERACTION. JRNL REF J.MED.CHEM. V. 64 11614 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34313116 JRNL DOI 10.1021/ACS.JMEDCHEM.1C00957 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15RC3_3435: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29563 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1462 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.9493 - 4.7382 1.00 3006 154 0.1935 0.2158 REMARK 3 2 4.7382 - 3.7614 1.00 2856 146 0.1722 0.2008 REMARK 3 3 3.7614 - 3.2861 1.00 2819 152 0.2086 0.2649 REMARK 3 4 3.2861 - 2.9857 1.00 2835 120 0.2315 0.2900 REMARK 3 5 2.9857 - 2.7718 1.00 2767 153 0.2419 0.3099 REMARK 3 6 2.7718 - 2.6084 1.00 2781 146 0.2512 0.2893 REMARK 3 7 2.6084 - 2.4777 1.00 2776 150 0.2551 0.3453 REMARK 3 8 2.4777 - 2.3699 1.00 2743 148 0.2442 0.2785 REMARK 3 9 2.3699 - 2.2787 1.00 2738 148 0.2508 0.2904 REMARK 3 10 2.2787 - 2.2000 1.00 2780 145 0.2720 0.3476 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.022 4049 REMARK 3 ANGLE : 1.852 5506 REMARK 3 CHIRALITY : 0.143 616 REMARK 3 PLANARITY : 0.007 693 REMARK 3 DIHEDRAL : 25.692 1410 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6R3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-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 : 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) : 0.91842 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29563 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 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: 5C3T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M TRIS PH 8.4 CONTAINING 0.28 M REMARK 280 SODIUM CHLORIDE AND 27% (W/V) PEG 4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 20.26350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.05800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.30450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.05800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.26350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.30450 REMARK 290 SMTRY3 4 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, D 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 HIS A 144 REMARK 465 HIS A 145 REMARK 465 HIS B 143 REMARK 465 HIS B 144 REMARK 465 HIS B 145 REMARK 465 HIS C 143 REMARK 465 HIS C 144 REMARK 465 HIS C 145 REMARK 465 HIS D 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 LYS A 46 CB CG CD CE NZ REMARK 470 GLN A 47 CG CD OE1 NE2 REMARK 470 GLU A 71 CG CD OE1 OE2 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 CG CD OE1 NE2 REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 GLN A 107 CG CD OE1 NE2 REMARK 470 LYS A 129 CG CD CE NZ REMARK 470 HIS A 143 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 45 CB CG CD OE1 OE2 REMARK 470 LYS B 46 CB CG CD CE NZ REMARK 470 GLN B 47 CG CD OE1 NE2 REMARK 470 ASP B 61 CG OD1 OD2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 ASP B 73 CG OD1 OD2 REMARK 470 LEU B 74 CG CD1 CD2 REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 LYS B 89 CG CD CE NZ REMARK 470 GLN B 107 CG CD OE1 NE2 REMARK 470 GLU C 45 CB CG CD OE1 OE2 REMARK 470 LYS C 46 CB CG CD CE NZ REMARK 470 GLN C 47 CG CD OE1 NE2 REMARK 470 LEU C 50 CG CD1 CD2 REMARK 470 ASN C 63 CG OD1 ND2 REMARK 470 GLU C 71 CG CD OE1 OE2 REMARK 470 LYS C 75 CG CD CE NZ REMARK 470 VAL C 76 CG1 CG2 REMARK 470 ARG C 82 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 83 CG CD OE1 NE2 REMARK 470 LYS C 105 CG CD CE NZ REMARK 470 GLN C 107 CG CD OE1 NE2 REMARK 470 GLU D 45 CB CG CD OE1 OE2 REMARK 470 LYS D 46 CB CG CD CE NZ REMARK 470 GLN D 47 CG CD OE1 NE2 REMARK 470 GLU D 71 CG CD OE1 OE2 REMARK 470 ASP D 73 CG OD1 OD2 REMARK 470 LEU D 74 CG CD1 CD2 REMARK 470 LYS D 75 CG CD CE NZ REMARK 470 GLN D 77 CG CD OE1 NE2 REMARK 470 ARG D 82 CG CD NE CZ NH1 NH2 REMARK 470 GLN D 83 CG CD OE1 NE2 REMARK 470 ARG D 113 CG CD NE CZ NH1 NH2 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 SG CYS C 40 SG CYS C 114 1.45 REMARK 500 NH2 ARG C 125 OD1 ASP D 61 1.49 REMARK 500 SG CYS D 40 SG CYS D 114 1.73 REMARK 500 SG CYS B 40 SG CYS B 114 1.80 REMARK 500 OD1 ASP D 61 O HOH D 301 1.90 REMARK 500 NE2 GLN D 66 CB ASP D 73 1.90 REMARK 500 OE1 GLN D 100 O HOH D 302 1.96 REMARK 500 OG1 THR A 102 O HOH A 301 1.98 REMARK 500 OE2 GLU C 60 O HOH C 301 2.00 REMARK 500 O45 JQT D 201 O HOH D 303 2.05 REMARK 500 OH TYR B 56 O HOH B 301 2.06 REMARK 500 OE1 GLU A 58 O HOH A 302 2.11 REMARK 500 O ALA B 52 O HOH B 302 2.13 REMARK 500 OD1 ASP A 61 NH2 ARG B 113 2.15 REMARK 500 O HOH A 358 O HOH A 361 2.16 REMARK 500 O HOH A 326 O HOH A 367 2.17 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 NH1 ARG B 86 OE2 GLU C 139 4555 2.06 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 -102.81 -86.66 REMARK 500 ASP A 61 -0.36 75.95 REMARK 500 TYR A 118 85.34 -157.38 REMARK 500 LYS B 46 -66.71 -134.86 REMARK 500 ASP B 61 -4.50 77.62 REMARK 500 GLN B 83 -1.89 75.78 REMARK 500 TYR B 118 78.29 -155.52 REMARK 500 GLN C 83 -6.56 85.79 REMARK 500 LYS D 46 -135.33 59.14 REMARK 500 ASP D 61 -4.86 81.50 REMARK 500 LEU D 74 -64.40 65.85 REMARK 500 GLN D 83 -14.26 89.52 REMARK 500 TYR D 118 85.93 -151.90 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 EDO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JQT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JQT D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ASP D 61 and ARG C REMARK 800 125 DBREF 6R3K A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 6R3K B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 6R3K C 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 6R3K D 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 SEQADV 6R3K ALA A 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA A 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA A 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K LEU A 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K GLU A 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS A 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS A 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS A 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS A 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS A 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS A 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA B 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA B 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA B 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K LEU B 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K GLU B 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS B 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS B 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS B 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS B 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS B 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS B 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA C 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA C 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA C 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K LEU C 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K GLU C 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS C 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS C 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS C 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS C 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS C 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS C 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA D 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA D 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K ALA D 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K LEU D 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K GLU D 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS D 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS D 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS D 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS D 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS D 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6R3K HIS D 145 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 A 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 A 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 B 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 B 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 B 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 B 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 B 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 B 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 B 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 B 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 B 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 C 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 C 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 C 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 C 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 C 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 C 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 C 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 C 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 C 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 D 128 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 D 128 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 D 128 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 D 128 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 D 128 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 D 128 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 D 128 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 D 128 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 D 128 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 D 128 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET EDO A 201 4 HET JQT B 201 46 HET EDO C 201 4 HET JQT D 201 46 HETNAM EDO 1,2-ETHANEDIOL HETNAM JQT (2~{S},4~{R})-1-[[5-CHLORANYL-2-[(3-CYANOPHENYL) HETNAM 2 JQT METHOXY]-4-[[3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-2- HETNAM 3 JQT METHYL-PHENYL]METHOXY]PHENYL]METHYL]-4-OXIDANYL- HETNAM 4 JQT PYRROLIDINE-2-CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 2(C2 H6 O2) FORMUL 6 JQT 2(C36 H33 CL N2 O7) FORMUL 9 HOH *248(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 LEU A 88 SER A 93 1 6 HELIX 4 AA4 LYS A 105 ALA A 109 5 5 HELIX 5 AA5 PRO A 133 HIS A 143 1 11 HELIX 6 AA6 ASP B 49 LEU B 53 5 5 HELIX 7 AA7 LEU B 74 GLN B 77 5 4 HELIX 8 AA8 HIS B 78 ARG B 82 5 5 HELIX 9 AA9 LEU B 88 SER B 93 1 6 HELIX 10 AB1 LYS B 105 ALA B 109 5 5 HELIX 11 AB2 PRO B 133 HIS B 142 1 10 HELIX 12 AB3 ASP C 49 ALA C 51 5 3 HELIX 13 AB4 HIS C 78 ARG C 82 5 5 HELIX 14 AB5 LYS C 89 LEU C 94 5 6 HELIX 15 AB6 LYS C 105 ALA C 109 5 5 HELIX 16 AB7 PRO C 133 HIS C 142 1 10 HELIX 17 AB8 ASP D 49 ALA D 52 5 4 HELIX 18 AB9 HIS D 78 ARG D 82 5 5 HELIX 19 AC1 LEU D 88 SER D 93 1 6 HELIX 20 AC2 LYS D 105 ALA D 109 5 5 HELIX 21 AC3 PRO D 133 HIS D 144 1 12 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 VAL A 30 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 6 LEU B 27 GLU B 31 0 SHEET 2 AA3 6 ALA B 121 ASN B 131 1 O LYS B 129 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 VAL C 30 SHEET 3 AA5 6 GLY C 110 TYR C 118 -1 N TYR C 112 O ILE C 126 SHEET 4 AA5 6 LEU C 53 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 LEU C 99 N ILE C 38 SHEET 3 AA6 3 ALA C 85 LEU C 87 -1 N ARG C 86 O GLN C 100 SHEET 1 AA7 6 LEU D 27 GLU D 31 0 SHEET 2 AA7 6 ALA D 121 ASN D 131 1 O LYS D 129 N TYR D 28 SHEET 3 AA7 6 GLY D 110 SER D 117 -1 N TYR D 112 O ILE D 126 SHEET 4 AA7 6 ILE D 54 MET D 59 -1 N TYR D 56 O MET D 115 SHEET 5 AA7 6 LYS D 62 VAL D 68 -1 O ILE D 64 N TRP D 57 SHEET 6 AA7 6 GLU D 71 GLU D 72 -1 O GLU D 71 N VAL D 68 SHEET 1 AA8 3 MET D 36 LYS D 41 0 SHEET 2 AA8 3 ASN D 96 ILE D 101 -1 O ALA D 97 N CYS D 40 SHEET 3 AA8 3 ALA D 85 LEU D 87 -1 N ARG D 86 O GLN D 100 SSBOND 1 CYS A 40 CYS A 114 1555 1555 1.84 SITE 1 AC1 5 LEU A 106 ALA A 109 VAL A 130 HOH A 326 SITE 2 AC1 5 HOH A 345 SITE 1 AC2 17 THR A 20 ILE A 54 TYR A 56 MET A 115 SITE 2 AC2 17 ALA A 121 ASP A 122 TYR A 123 LYS A 124 SITE 3 AC2 17 ARG A 125 ILE B 54 TYR B 56 GLN B 66 SITE 4 AC2 17 VAL B 68 MET B 115 ALA B 121 ASP B 122 SITE 5 AC2 17 HOH B 349 SITE 1 AC3 5 ASP C 122 TYR D 56 GLN D 66 VAL D 68 SITE 2 AC3 5 JQT D 201 SITE 1 AC4 18 TYR C 56 VAL C 68 MET C 115 ALA C 121 SITE 2 AC4 18 ASP C 122 EDO C 201 PHE D 19 THR D 20 SITE 3 AC4 18 ILE D 54 TYR D 56 MET D 115 ALA D 121 SITE 4 AC4 18 ASP D 122 TYR D 123 LYS D 124 ARG D 125 SITE 5 AC4 18 HOH D 303 HOH D 322 SITE 1 AC5 21 MET C 59 GLU C 60 LYS C 62 TYR C 112 SITE 2 AC5 21 ARG C 113 TYR C 123 LYS C 124 ILE C 126 SITE 3 AC5 21 HOH C 303 HOH C 304 MET D 59 GLU D 60 SITE 4 AC5 21 LYS D 62 ASN D 63 TYR D 112 LYS D 124 SITE 5 AC5 21 ILE D 126 JQT D 201 HOH D 301 HOH D 321 SITE 6 AC5 21 HOH D 322 CRYST1 40.527 84.609 164.116 90.00 90.00 90.00 P 21 21 21 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 0.024675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006093 0.00000