HEADER IMMUNE SYSTEM 10-OCT-19 6UMT TITLE HIGH-AFFINITY HUMAN PD-1 PD-L2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 33-150; COMPND 5 SYNONYM: HPD-1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: PROGRAMMED DEATH LIGAND 2,BUTYROPHILIN B7-DC,B7-DC; COMPND 12 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: PDCD1, PD1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: EXPI293F; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PDCD1LG2, B7DC, CD273, PDCD1L2, PDL2; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: EXPI293F KEYWDS PD-1, PD-L2, IMMUNE CHECKPOINT, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.TANG,P.S.KIM REVDAT 3 11-OCT-23 6UMT 1 LINK REVDAT 2 18-DEC-19 6UMT 1 JRNL REVDAT 1 27-NOV-19 6UMT 0 JRNL AUTH S.TANG,P.S.KIM JRNL TITL A HIGH-AFFINITY HUMAN PD-1/PD-L2 COMPLEX INFORMS AVENUES FOR JRNL TITL 2 SMALL-MOLECULE IMMUNE CHECKPOINT DRUG DISCOVERY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 24500 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31727844 JRNL DOI 10.1073/PNAS.1916916116 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 17743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1774 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 37.5080 - 4.6666 0.99 1343 149 0.1928 0.1928 REMARK 3 2 4.6666 - 3.7051 1.00 1282 143 0.1528 0.1855 REMARK 3 3 3.7051 - 3.2371 1.00 1261 139 0.1892 0.2142 REMARK 3 4 3.2371 - 2.9412 1.00 1238 138 0.2030 0.2477 REMARK 3 5 2.9412 - 2.7305 1.00 1244 139 0.2237 0.2390 REMARK 3 6 2.7305 - 2.5695 1.00 1243 138 0.2136 0.2682 REMARK 3 7 2.5695 - 2.4409 1.00 1230 136 0.2209 0.2560 REMARK 3 8 2.4409 - 2.3346 1.00 1234 137 0.2075 0.2666 REMARK 3 9 2.3346 - 2.2448 0.99 1221 136 0.2260 0.2638 REMARK 3 10 2.2448 - 2.1673 1.00 1224 136 0.2341 0.2588 REMARK 3 11 2.1673 - 2.0996 0.98 1200 133 0.2527 0.3290 REMARK 3 12 2.0996 - 2.0395 0.95 1159 129 0.2655 0.3018 REMARK 3 13 2.0395 - 1.9860 0.90 1090 121 0.2965 0.3448 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.76 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 : 0.014 1687 REMARK 3 ANGLE : 1.910 2298 REMARK 3 CHIRALITY : 0.111 265 REMARK 3 PLANARITY : 0.011 297 REMARK 3 DIHEDRAL : 12.800 613 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 6UMT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000244862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-19 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17793 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.986 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.76100 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRIES 3RRQ & 3BP5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MAGNESIUM ACETATE, 10% W/V REMARK 280 PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 20.64550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.85050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.89900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.85050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.64550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.89900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL 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 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 14 REMARK 465 GLY A 15 REMARK 465 TRP A 16 REMARK 465 SER A 17 REMARK 465 CYS A 18 REMARK 465 ILE A 19 REMARK 465 ILE A 20 REMARK 465 LEU A 21 REMARK 465 PHE A 22 REMARK 465 LEU A 23 REMARK 465 VAL A 24 REMARK 465 ALA A 25 REMARK 465 THR A 26 REMARK 465 ALA A 27 REMARK 465 THR A 28 REMARK 465 GLY A 29 REMARK 465 VAL A 30 REMARK 465 HIS A 31 REMARK 465 SER A 32 REMARK 465 ASP A 85 REMARK 465 ARG A 86 REMARK 465 SER A 87 REMARK 465 GLN A 88 REMARK 465 PRO A 89 REMARK 465 GLY A 90 REMARK 465 GLN A 91 REMARK 465 ASP A 92 REMARK 465 GLU A 150 REMARK 465 PRO A 151 REMARK 465 GLU A 152 REMARK 465 ALA A 153 REMARK 465 MET B 1 REMARK 465 ILE B 2 REMARK 465 PHE B 3 REMARK 465 LEU B 4 REMARK 465 LEU B 5 REMARK 465 LEU B 6 REMARK 465 MET B 7 REMARK 465 LEU B 8 REMARK 465 SER B 9 REMARK 465 LEU B 10 REMARK 465 GLU B 11 REMARK 465 LEU B 12 REMARK 465 GLN B 13 REMARK 465 LEU B 14 REMARK 465 HIS B 15 REMARK 465 GLN B 16 REMARK 465 ILE B 17 REMARK 465 ALA B 18 REMARK 465 ALA B 19 REMARK 465 ASP B 65 REMARK 465 THR B 66 REMARK 465 SER B 67 REMARK 465 SER B 122 REMARK 465 TYR B 123 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 131 CE NZ REMARK 470 LYS A 135 CE NZ REMARK 470 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 45 CG OD1 OD2 REMARK 470 SER B 48 OG REMARK 470 HIS B 49 CG ND1 CD2 CE1 NE2 REMARK 470 VAL B 50 CG1 CG2 REMARK 470 ASN B 51 CG OD1 ND2 REMARK 470 LEU B 52 CG CD1 CD2 REMARK 470 GLU B 63 CG CD OE1 OE2 REMARK 470 ASP B 64 CG OD1 OD2 REMARK 470 ARG B 70 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 118 CD CE NZ 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 211 O HOH B 244 1.47 REMARK 500 O HOH A 313 O HOH A 316 1.63 REMARK 500 O HOH A 301 O HOH A 354 2.00 REMARK 500 ND1 HIS A 107 O HOH A 301 2.19 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 CB SER A 60 OE2 GLU A 141 3445 1.68 REMARK 500 OG SER A 60 OE2 GLU A 141 3445 1.79 REMARK 500 O HOH A 358 O HOH B 215 3555 2.16 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 LEU B 52 N - CA - C ANGL. DEV. = 23.9 DEGREES REMARK 500 HIS B 69 N - CA - C ANGL. DEV. = 17.8 DEGREES REMARK 500 ARG B 70 C - N - CA ANGL. DEV. = -18.1 DEGREES REMARK 500 ARG B 70 N - CA - C ANGL. DEV. = -22.6 DEGREES REMARK 500 GLU B 71 CA - C - N ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG B 72 C - N - CA ANGL. DEV. = 15.9 DEGREES REMARK 500 ARG B 72 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 72 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 72 N - CA - C ANGL. DEV. = 23.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 62 PHE A 63 -108.27 REMARK 500 LEU B 52 GLY B 53 115.70 REMARK 500 ARG B 70 GLU B 71 -126.89 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 VAL B 50 10.79 REMARK 500 GLU B 71 15.49 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 373 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH B 251 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH B 252 DISTANCE = 8.39 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 46 OE1 REMARK 620 2 GLU A 46 OE2 58.4 REMARK 620 3 GLU A 146 OE1 91.7 78.6 REMARK 620 4 GLU A 146 OE2 129.4 75.6 57.2 REMARK 620 5 ASP B 37 OD2 67.0 119.7 79.7 131.4 REMARK 620 6 HIS B 88 NE2 64.8 118.4 81.4 133.9 2.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 DBREF 6UMT A 33 150 UNP Q15116 PDCD1_HUMAN 33 150 DBREF 6UMT B 1 123 UNP Q9BQ51 PD1L2_HUMAN 1 123 SEQADV 6UMT MET A 14 UNP Q15116 EXPRESSION TAG SEQADV 6UMT GLY A 15 UNP Q15116 EXPRESSION TAG SEQADV 6UMT TRP A 16 UNP Q15116 EXPRESSION TAG SEQADV 6UMT SER A 17 UNP Q15116 EXPRESSION TAG SEQADV 6UMT CYS A 18 UNP Q15116 EXPRESSION TAG SEQADV 6UMT ILE A 19 UNP Q15116 EXPRESSION TAG SEQADV 6UMT ILE A 20 UNP Q15116 EXPRESSION TAG SEQADV 6UMT LEU A 21 UNP Q15116 EXPRESSION TAG SEQADV 6UMT PHE A 22 UNP Q15116 EXPRESSION TAG SEQADV 6UMT LEU A 23 UNP Q15116 EXPRESSION TAG SEQADV 6UMT VAL A 24 UNP Q15116 EXPRESSION TAG SEQADV 6UMT ALA A 25 UNP Q15116 EXPRESSION TAG SEQADV 6UMT THR A 26 UNP Q15116 EXPRESSION TAG SEQADV 6UMT ALA A 27 UNP Q15116 EXPRESSION TAG SEQADV 6UMT THR A 28 UNP Q15116 EXPRESSION TAG SEQADV 6UMT GLY A 29 UNP Q15116 EXPRESSION TAG SEQADV 6UMT VAL A 30 UNP Q15116 EXPRESSION TAG SEQADV 6UMT HIS A 31 UNP Q15116 EXPRESSION TAG SEQADV 6UMT SER A 32 UNP Q15116 EXPRESSION TAG SEQADV 6UMT SER A 49 UNP Q15116 ASN 49 CONFLICT SEQADV 6UMT SER A 58 UNP Q15116 ASN 58 CONFLICT SEQADV 6UMT GLY A 74 UNP Q15116 ASN 74 ENGINEERED MUTATION SEQADV 6UMT PRO A 76 UNP Q15116 THR 76 ENGINEERED MUTATION SEQADV 6UMT SER A 93 UNP Q15116 CYS 93 CONFLICT SEQADV 6UMT ASP A 116 UNP Q15116 ASN 116 CONFLICT SEQADV 6UMT VAL A 132 UNP Q15116 ALA 132 ENGINEERED MUTATION SEQADV 6UMT PRO A 151 UNP Q15116 EXPRESSION TAG SEQADV 6UMT GLU A 152 UNP Q15116 EXPRESSION TAG SEQADV 6UMT ALA A 153 UNP Q15116 EXPRESSION TAG SEQADV 6UMT ASP B 37 UNP Q9BQ51 ASN 37 CONFLICT SEQADV 6UMT ASP B 64 UNP Q9BQ51 ASN 64 CONFLICT SEQRES 1 A 140 MET GLY TRP SER CYS ILE ILE LEU PHE LEU VAL ALA THR SEQRES 2 A 140 ALA THR GLY VAL HIS SER ASN PRO PRO THR PHE SER PRO SEQRES 3 A 140 ALA LEU LEU VAL VAL THR GLU GLY ASP SER ALA THR PHE SEQRES 4 A 140 THR CYS SER PHE SER SER THR SER GLU SER PHE VAL LEU SEQRES 5 A 140 ASN TRP TYR ARG MET SER PRO SER GLY GLN PRO ASP LYS SEQRES 6 A 140 LEU ALA ALA PHE PRO GLU ASP ARG SER GLN PRO GLY GLN SEQRES 7 A 140 ASP SER ARG PHE ARG VAL THR GLN LEU PRO ASN GLY ARG SEQRES 8 A 140 ASP PHE HIS MET SER VAL VAL ARG ALA ARG ARG ASP ASP SEQRES 9 A 140 SER GLY THR TYR LEU CYS GLY ALA ILE SER LEU ALA PRO SEQRES 10 A 140 LYS VAL GLN ILE LYS GLU SER LEU ARG ALA GLU LEU ARG SEQRES 11 A 140 VAL THR GLU ARG ARG ALA GLU PRO GLU ALA SEQRES 1 B 123 MET ILE PHE LEU LEU LEU MET LEU SER LEU GLU LEU GLN SEQRES 2 B 123 LEU HIS GLN ILE ALA ALA LEU PHE THR VAL THR VAL PRO SEQRES 3 B 123 LYS GLU LEU TYR ILE ILE GLU HIS GLY SER ASP VAL THR SEQRES 4 B 123 LEU GLU CYS ASN PHE ASP THR GLY SER HIS VAL ASN LEU SEQRES 5 B 123 GLY ALA ILE THR ALA SER LEU GLN LYS VAL GLU ASP ASP SEQRES 6 B 123 THR SER PRO HIS ARG GLU ARG ALA THR LEU LEU GLU GLU SEQRES 7 B 123 GLN LEU PRO LEU GLY LYS ALA SER PHE HIS ILE PRO GLN SEQRES 8 B 123 VAL GLN VAL ARG ASP GLU GLY GLN TYR GLN CYS ILE ILE SEQRES 9 B 123 ILE TYR GLY VAL ALA TRP ASP TYR LYS TYR LEU THR LEU SEQRES 10 B 123 LYS VAL LYS ALA SER TYR HET MG A 201 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 HOH *125(H2 O) HELIX 1 AA1 ARG A 114 SER A 118 5 5 HELIX 2 AA2 GLU B 77 LEU B 82 5 6 HELIX 3 AA3 GLN B 93 GLU B 97 5 5 SHEET 1 AA1 4 THR A 36 SER A 38 0 SHEET 2 AA1 4 ALA A 50 SER A 55 -1 O THR A 53 N SER A 38 SHEET 3 AA1 4 ASP A 105 VAL A 110 -1 O MET A 108 N PHE A 52 SHEET 4 AA1 4 PHE A 95 GLN A 99 -1 N ARG A 96 O SER A 109 SHEET 1 AA2 5 LEU A 41 THR A 45 0 SHEET 2 AA2 5 ALA A 140 THR A 145 1 O GLU A 141 N LEU A 42 SHEET 3 AA2 5 GLY A 119 SER A 127 -1 N GLY A 119 O LEU A 142 SHEET 4 AA2 5 LEU A 65 MET A 70 -1 N TYR A 68 O LEU A 122 SHEET 5 AA2 5 PRO A 76 PHE A 82 -1 O ASP A 77 N ARG A 69 SHEET 1 AA3 4 LEU A 41 THR A 45 0 SHEET 2 AA3 4 ALA A 140 THR A 145 1 O GLU A 141 N LEU A 42 SHEET 3 AA3 4 GLY A 119 SER A 127 -1 N GLY A 119 O LEU A 142 SHEET 4 AA3 4 GLN A 133 GLU A 136 -1 O LYS A 135 N ALA A 125 SHEET 1 AA4 4 THR B 22 THR B 24 0 SHEET 2 AA4 4 VAL B 38 ASP B 45 -1 O ASN B 43 N THR B 24 SHEET 3 AA4 4 LYS B 84 ILE B 89 -1 O ALA B 85 N CYS B 42 SHEET 4 AA4 4 THR B 74 LEU B 75 -1 N THR B 74 O HIS B 88 SHEET 1 AA5 4 LEU B 29 GLU B 33 0 SHEET 2 AA5 4 ALA B 109 LYS B 120 1 O LYS B 118 N TYR B 30 SHEET 3 AA5 4 GLY B 98 TYR B 106 -1 N TYR B 106 O ALA B 109 SHEET 4 AA5 4 ILE B 55 LYS B 61 -1 N SER B 58 O ILE B 103 SSBOND 1 CYS A 54 CYS A 123 1555 1555 2.04 SSBOND 2 CYS B 42 CYS B 102 1555 1555 2.07 LINK OE1 GLU A 46 MG MG A 201 1555 1555 2.11 LINK OE2 GLU A 46 MG MG A 201 1555 1555 2.43 LINK OE1 GLU A 146 MG MG A 201 1555 1555 2.51 LINK OE2 GLU A 146 MG MG A 201 1555 1555 1.99 LINK MG MG A 201 OD2 ASP B 37 3545 1555 1.99 LINK MG MG A 201 NE2 HIS B 88 3545 1555 2.01 CISPEP 1 SER A 38 PRO A 39 0 0.57 CISPEP 2 PHE A 82 PRO A 83 0 -12.83 CISPEP 3 ALA A 129 PRO A 130 0 2.34 SITE 1 AC1 4 GLU A 46 GLU A 146 ASP B 37 HIS B 88 CRYST1 41.291 67.798 89.701 90.00 90.00 90.00 P 21 21 21 4 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 0.024218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011148 0.00000