HEADER IMMUNE SYSTEM 27-MAR-17 5NIU 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 2 17-JAN-24 5NIU 1 REMARK REVDAT 1 06-DEC-17 5NIU 0 JRNL AUTH L.SKALNIAK,K.M.ZAK,K.GUZIK,K.MAGIERA,B.MUSIELAK,M.PACHOTA, JRNL AUTH 2 B.SZELAZEK,J.KOCIK,P.GRUDNIK,M.TOMALA,S.KRZANIK,K.PYRC, JRNL AUTH 3 A.DOMLING,G.DUBIN,T.A.HOLAK JRNL TITL SMALL-MOLECULE INHIBITORS OF PD-1/PD-L1 IMMUNE CHECKPOINT JRNL TITL 2 ALLEVIATE THE PD-L1-INDUCED EXHAUSTION OF T-CELLS. JRNL REF ONCOTARGET V. 8 72167 2017 JRNL REFN ESSN 1949-2553 JRNL PMID 29069777 JRNL DOI 10.18632/ONCOTARGET.20050 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35934 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1846 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.43000 REMARK 3 B22 (A**2) : -1.08000 REMARK 3 B33 (A**2) : -1.35000 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 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5NIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-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 : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : 37778 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 46.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 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 (%): 48.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5 CONTAINING 0.2 M REMARK 280 MAGNESIUM CHLORIDE AND 30% (W/V) PEG 4000, VAPOR DIFFUSION, REMARK 280 SITTING 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 19.94100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.20250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.33650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.20250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.94100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.33650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLU A 45 CG CD OE1 OE2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 GLN A 47 CG CD OE1 NE2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LEU A 74 CG CD1 CD2 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 HIS A 143 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 45 CG CD OE1 OE2 REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 GLN B 47 CG CD OE1 NE2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 LEU B 74 CG CD1 CD2 REMARK 470 LYS B 75 CD CE NZ REMARK 470 ARG B 86 CD NE CZ NH1 NH2 REMARK 470 GLN B 107 CG CD OE1 NE2 REMARK 470 HIS B 142 CG ND1 CD2 CE1 NE2 REMARK 470 GLU C 45 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 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 LYS C 105 CG CD CE NZ REMARK 470 HIS C 143 CG ND1 CD2 CE1 NE2 REMARK 470 GLU D 45 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 ASN D 63 CG OD1 ND2 REMARK 470 GLU D 71 CG CD OE1 OE2 REMARK 470 LYS D 75 CG CD CE NZ REMARK 470 GLN D 77 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 HIS D 144 CG ND1 CD2 CE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 58 N CA C O CB CG CD REMARK 480 GLU A 58 OE1 OE2 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 O HOH B 266 O HOH B 277 1.98 REMARK 500 CB GLU A 45 O HOH A 367 1.98 REMARK 500 O HOH B 224 O HOH B 277 2.00 REMARK 500 O ASP A 61 O HOH A 301 2.05 REMARK 500 NH1 ARG A 125 O HOH A 302 2.05 REMARK 500 O LEU C 138 O HIS C 141 2.09 REMARK 500 O HOH D 353 O HOH D 385 2.10 REMARK 500 OE2 GLU A 72 O HOH A 303 2.11 REMARK 500 NE2 GLN B 100 O HOH B 201 2.13 REMARK 500 O HOH C 304 O HOH C 344 2.17 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 CYS A 40 CB CYS A 40 SG -0.107 REMARK 500 GLU A 60 CD GLU A 60 OE2 0.073 REMARK 500 CYS B 40 CB CYS B 40 SG -0.158 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 B 40 N - CA - CB ANGL. DEV. = -12.8 DEGREES REMARK 500 GLU B 139 C - N - CA ANGL. DEV. = 15.2 DEGREES REMARK 500 GLU B 139 N - CA - C ANGL. DEV. = -24.1 DEGREES REMARK 500 MET D 59 CG - SD - CE ANGL. DEV. = 11.0 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 LYS A 46 -123.98 57.49 REMARK 500 ASP A 61 -3.06 71.81 REMARK 500 TYR A 118 79.91 -158.61 REMARK 500 LYS B 46 -148.73 -134.62 REMARK 500 GLN B 47 127.52 -33.54 REMARK 500 GLN B 83 -5.56 74.03 REMARK 500 TYR B 118 79.22 -161.03 REMARK 500 ASP C 61 -3.90 72.62 REMARK 500 GLN C 83 -5.22 72.44 REMARK 500 TYR C 118 79.10 -156.35 REMARK 500 LYS D 46 -162.12 -103.75 REMARK 500 ASP D 61 -6.03 72.14 REMARK 500 TYR D 118 79.57 -159.79 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 8YZ A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 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 8YZ D 201 DBREF 5NIU A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 5NIU B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 5NIU C 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 5NIU D 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 SEQADV 5NIU ALA A 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA A 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA A 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU LEU A 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU GLU A 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS A 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS A 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS A 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS A 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS A 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS A 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA B 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA B 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA B 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU LEU B 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU GLU B 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS B 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS B 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS B 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS B 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS B 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS B 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA C 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA C 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA C 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU LEU C 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU GLU C 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS C 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS C 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS C 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS C 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS C 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS C 145 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA D 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA D 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU ALA D 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU LEU D 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU GLU D 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS D 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS D 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS D 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS D 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU HIS D 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5NIU 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 8YZ A 201 44 HET EDO A 202 4 HET EDO C 201 4 HET 8YZ D 201 44 HETNAM 8YZ (2~{R})-2-[[2-[(3-CYANOPHENYL)METHOXY]-4-[[3-(2,3- HETNAM 2 8YZ DIHYDRO-1,4-BENZODIOXIN-6-YL)-2-METHYL- HETNAM 3 8YZ PHENYL]METHOXY]-5-METHYL-PHENYL]METHYLAMINO]-3- HETNAM 4 8YZ OXIDANYL-PROPANOIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 8YZ 2(C35 H34 N2 O7) FORMUL 6 EDO 2(C2 H6 O2) FORMUL 9 HOH *318(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 ALA B 52 5 4 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 LEU B 138 1 6 HELIX 12 AB3 ASP C 49 ALA C 52 5 4 HELIX 13 AB4 LEU C 74 GLN C 77 5 4 HELIX 14 AB5 HIS C 78 ARG C 82 5 5 HELIX 15 AB6 LYS C 89 LEU C 94 5 6 HELIX 16 AB7 LYS C 105 ALA C 109 5 5 HELIX 17 AB8 PRO C 133 HIS C 141 1 9 HELIX 18 AB9 ASP D 49 ALA D 52 5 4 HELIX 19 AC1 LEU D 74 GLN D 77 5 4 HELIX 20 AC2 HIS D 78 ARG D 82 5 5 HELIX 21 AC3 LYS D 89 LEU D 94 5 6 HELIX 22 AC4 LYS D 105 ALA D 109 5 5 HELIX 23 AC5 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 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 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 ILE B 101 N MET B 36 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 ALA C 97 N CYS C 40 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 PHE D 67 N VAL D 55 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 2.01 SSBOND 2 CYS B 40 CYS B 114 1555 1555 2.06 SSBOND 3 CYS C 40 CYS C 114 1555 1555 2.03 SSBOND 4 CYS D 40 CYS D 114 1555 1555 2.02 SITE 1 AC1 19 THR A 20 ILE A 54 TYR A 56 ALA A 121 SITE 2 AC1 19 ASP A 122 TYR A 123 LYS A 124 ARG A 125 SITE 3 AC1 19 EDO A 202 HOH A 327 HOH A 331 ILE B 54 SITE 4 AC1 19 TYR B 56 GLN B 66 VAL B 68 MET B 115 SITE 5 AC1 19 ALA B 121 ASP B 122 HOH B 225 SITE 1 AC2 6 TYR A 56 8YZ A 201 HOH A 306 ASP B 122 SITE 2 AC2 6 TYR B 123 HOH B 266 SITE 1 AC3 4 ASP C 122 HOH C 315 HOH C 324 8YZ D 201 SITE 1 AC4 16 ILE C 54 TYR C 56 ASP C 61 GLN C 66 SITE 2 AC4 16 VAL C 68 MET C 115 ASP C 122 EDO C 201 SITE 3 AC4 16 THR D 20 ILE D 54 TYR D 56 MET D 115 SITE 4 AC4 16 ALA D 121 ASP D 122 TYR D 123 LYS D 124 CRYST1 39.882 84.673 164.405 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 0.025074 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006083 0.00000