HEADER IMMUNE SYSTEM 29-APR-17 5XJ4 TITLE COMPLEX STRUCTURE OF DURVALUMAB-SCFV/PD-L1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DURVALUMAB-VH; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DURVALUMAB-VL; COMPND 12 CHAIN: L; COMPND 13 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; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DURVALUMAB, PD-L1, COMPLEX STRUCTURE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.TAN,K.LIU,Y.CHAI,G.F.GAO,J.QI REVDAT 3 09-OCT-24 5XJ4 1 REMARK REVDAT 2 22-NOV-23 5XJ4 1 REMARK REVDAT 1 25-APR-18 5XJ4 0 JRNL AUTH S.TAN,K.LIU,Y.CHAI,C.W.ZHANG,S.GAO,G.F.GAO,J.QI JRNL TITL DISTINCT PD-L1 BINDING CHARACTERISTICS OF THERAPEUTIC JRNL TITL 2 MONOCLONAL ANTIBODY DURVALUMAB JRNL REF PROTEIN CELL V. 9 135 2018 JRNL REFN ESSN 1674-8018 JRNL PMID 28488247 JRNL DOI 10.1007/S13238-017-0412-8 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 34942 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) : 0.216 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1743 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 42.3469 - 5.2477 1.00 2988 161 0.1806 0.1837 REMARK 3 2 5.2477 - 4.1665 1.00 2873 164 0.1504 0.1886 REMARK 3 3 4.1665 - 3.6401 1.00 2872 153 0.1764 0.1843 REMARK 3 4 3.6401 - 3.3074 1.00 2883 142 0.2034 0.2372 REMARK 3 5 3.3074 - 3.0705 1.00 2849 149 0.2289 0.2355 REMARK 3 6 3.0705 - 2.8895 1.00 2857 140 0.2411 0.2744 REMARK 3 7 2.8895 - 2.7448 1.00 2818 155 0.2499 0.2847 REMARK 3 8 2.7448 - 2.6253 1.00 2805 141 0.2653 0.3256 REMARK 3 9 2.6253 - 2.5243 1.00 2839 166 0.2676 0.3113 REMARK 3 10 2.5243 - 2.4372 1.00 2825 158 0.2699 0.2810 REMARK 3 11 2.4372 - 2.3610 0.93 2618 125 0.3428 0.4004 REMARK 3 12 2.3610 - 2.2935 0.69 1972 89 0.4565 0.5165 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.980 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 : 0.004 3532 REMARK 3 ANGLE : 0.946 4778 REMARK 3 CHIRALITY : 0.075 526 REMARK 3 PLANARITY : 0.005 612 REMARK 3 DIHEDRAL : 14.922 1283 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 1.0788 32.3001 78.5407 REMARK 3 T TENSOR REMARK 3 T11: 0.4473 T22: 0.3425 REMARK 3 T33: 0.1669 T12: 0.0742 REMARK 3 T13: 0.2015 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 0.0371 L22: 0.0221 REMARK 3 L33: 0.0841 L12: -0.0339 REMARK 3 L13: 0.0069 L23: 0.0461 REMARK 3 S TENSOR REMARK 3 S11: 0.0619 S12: -0.1438 S13: 0.1366 REMARK 3 S21: 0.0190 S22: 0.0103 S23: -0.0018 REMARK 3 S31: -0.2364 S32: 0.0192 S33: -0.0053 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN H REMARK 3 ORIGIN FOR THE GROUP (A): 31.2971 16.0107 59.4606 REMARK 3 T TENSOR REMARK 3 T11: 0.2615 T22: 0.2664 REMARK 3 T33: 0.1577 T12: 0.0972 REMARK 3 T13: 0.1210 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 0.0282 L22: 0.0093 REMARK 3 L33: 0.0639 L12: -0.0147 REMARK 3 L13: 0.0380 L23: -0.0252 REMARK 3 S TENSOR REMARK 3 S11: 0.1237 S12: -0.0390 S13: 0.0690 REMARK 3 S21: -0.0351 S22: 0.0039 S23: -0.0303 REMARK 3 S31: 0.0558 S32: 0.1597 S33: 0.1010 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN L REMARK 3 ORIGIN FOR THE GROUP (A): 16.3531 27.3830 47.6247 REMARK 3 T TENSOR REMARK 3 T11: 0.2659 T22: 0.1911 REMARK 3 T33: 0.1459 T12: 0.0806 REMARK 3 T13: 0.2019 T23: 0.1038 REMARK 3 L TENSOR REMARK 3 L11: 0.0064 L22: 0.0107 REMARK 3 L33: 0.0048 L12: -0.0060 REMARK 3 L13: 0.0023 L23: 0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.0410 S12: 0.0151 S13: 0.0780 REMARK 3 S21: -0.0600 S22: 0.0196 S23: -0.0274 REMARK 3 S31: -0.0810 S32: -0.0139 S33: 0.0204 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 5XJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1300003621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 17.80 REMARK 200 R MERGE FOR SHELL (I) : 4.41500 REMARK 200 R SYM FOR SHELL (I) : 4.41500 REMARK 200 <I/SIGMA(I)> 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: 3RRQ, 3EYQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, PH 7.0, REMARK 280 EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 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 0.00000 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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: H 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L 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 LYS A 185 REMARK 465 ARG A 186 REMARK 465 ASP A 215 REMARK 465 PRO A 216 REMARK 465 GLU A 217 REMARK 465 LEU A 229 REMARK 465 PRO A 230 REMARK 465 LEU A 231 REMARK 465 ALA A 232 REMARK 465 HIS A 233 REMARK 465 PRO A 234 REMARK 465 PRO A 235 REMARK 465 ASN A 236 REMARK 465 GLU A 237 REMARK 465 ARG A 238 REMARK 465 SER H 122 REMARK 465 SER L 114 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 LYS A 162 O HOH A 301 1.81 REMARK 500 O HOH A 351 O HOH A 353 1.83 REMARK 500 O HOH H 246 O HOH H 250 1.88 REMARK 500 O HOH A 320 O HOH A 346 1.93 REMARK 500 OD1 ASP H 63 O HOH H 201 1.93 REMARK 500 OD1 ASN A 183 O HOH A 302 1.97 REMARK 500 N LEU A 214 O HOH A 301 2.08 REMARK 500 O HOH L 211 O HOH L 261 2.08 REMARK 500 O ILE L 107 O HOH L 201 2.09 REMARK 500 OE2 GLU A 72 O HOH A 303 2.11 REMARK 500 O HOH L 258 O HOH L 260 2.13 REMARK 500 O LYS H 59 O HOH H 202 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 342 O HOH A 343 4556 2.18 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 SER A 184 N - CA - CB ANGL. DEV. = 14.7 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 -124.78 -145.75 REMARK 500 GLU A 60 -119.11 51.97 REMARK 500 ASP A 103 71.80 47.52 REMARK 500 TYR A 118 76.05 -157.65 REMARK 500 PRO A 161 -154.62 -82.53 REMARK 500 SER A 169 -157.67 -74.93 REMARK 500 HIS A 172 41.75 39.37 REMARK 500 THR A 182 -149.09 -128.88 REMARK 500 THR A 201 -168.33 -122.58 REMARK 500 ASN A 204 -10.94 91.50 REMARK 500 ALA H 108 -161.59 57.12 REMARK 500 SER L 31 19.17 59.32 REMARK 500 ALA L 52 -28.61 69.42 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 GLU A 188 LYS A 189 -143.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XJ3 RELATED DB: PDB DBREF 5XJ4 A 19 238 UNP Q9NZQ7 PD1L1_HUMAN 19 238 DBREF 5XJ4 H 2 122 PDB 5XJ4 5XJ4 2 122 DBREF 5XJ4 L 1 114 PDB 5XJ4 5XJ4 1 114 SEQADV 5XJ4 MET A 18 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 221 MET PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 221 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 221 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 221 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 221 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 A 221 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 221 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 221 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 221 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 A 221 ASN LYS ILE ASN GLN ARG ILE LEU VAL VAL ASP PRO VAL SEQRES 11 A 221 THR SER GLU HIS GLU LEU THR CYS GLN ALA GLU GLY TYR SEQRES 12 A 221 PRO LYS ALA GLU VAL ILE TRP THR SER SER ASP HIS GLN SEQRES 13 A 221 VAL LEU SER GLY LYS THR THR THR THR ASN SER LYS ARG SEQRES 14 A 221 GLU GLU LYS LEU PHE ASN VAL THR SER THR LEU ARG ILE SEQRES 15 A 221 ASN THR THR THR ASN GLU ILE PHE TYR CYS THR PHE ARG SEQRES 16 A 221 ARG LEU ASP PRO GLU GLU ASN HIS THR ALA GLU LEU VAL SEQRES 17 A 221 ILE PRO GLU LEU PRO LEU ALA HIS PRO PRO ASN GLU ARG SEQRES 1 H 121 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 121 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 121 PHE THR PHE SER ARG TYR TRP MET SER TRP VAL ARG GLN SEQRES 4 H 121 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ASN ILE LYS SEQRES 5 H 121 GLN ASP GLY SER GLU LYS TYR TYR VAL ASP SER VAL LYS SEQRES 6 H 121 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 121 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 121 ALA VAL TYR TYR CYS ALA ARG GLU GLY GLY TRP PHE GLY SEQRES 9 H 121 GLU LEU ALA PHE ASP TYR TRP GLY GLN GLY THR LEU VAL SEQRES 10 H 121 THR VAL SER SER SEQRES 1 L 114 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 114 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 114 GLN ARG VAL SER SER SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 L 114 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR ASP ALA SEQRES 5 L 114 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 L 114 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 L 114 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 L 114 TYR GLY SER LEU PRO TRP THR PHE GLY GLN GLY THR LYS SEQRES 9 L 114 VAL GLU ILE LYS ARG GLY GLY GLY GLY SER FORMUL 4 HOH *169(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 THR H 29 TYR H 33 5 5 HELIX 6 AA6 ASP H 63 LYS H 66 5 4 HELIX 7 AA7 ARG H 88 THR H 92 5 5 HELIX 8 AA8 VAL L 29 SER L 32 5 4 HELIX 9 AA9 GLU L 80 PHE L 84 5 5 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 GLY A 110 O VAL A 128 SHEET 4 AA1 6 ILE A 54 MET A 59 -1 N ILE A 54 O SER A 117 SHEET 5 AA1 6 LYS A 62 VAL A 68 -1 O LYS A 62 N MET A 59 SHEET 6 AA1 6 GLU A 71 GLU A 72 -1 O GLU A 71 N VAL A 68 SHEET 1 AA2 3 MET A 36 LYS A 41 0 SHEET 2 AA2 3 ASN A 96 ILE A 101 -1 O ALA A 97 N CYS A 40 SHEET 3 AA2 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100 SHEET 1 AA3 4 ASN A 138 ASP A 145 0 SHEET 2 AA3 4 GLU A 150 GLY A 159 -1 O GLU A 152 N LEU A 142 SHEET 3 AA3 4 PHE A 191 ASN A 200 -1 O VAL A 193 N ALA A 157 SHEET 4 AA3 4 LYS A 178 THR A 182 -1 N THR A 180 O THR A 194 SHEET 1 AA4 4 VAL A 174 LEU A 175 0 SHEET 2 AA4 4 ALA A 163 THR A 168 -1 N TRP A 167 O LEU A 175 SHEET 3 AA4 4 ILE A 206 ARG A 213 -1 O ARG A 212 N GLU A 164 SHEET 4 AA4 4 HIS A 220 VAL A 225 -1 O LEU A 224 N PHE A 207 SHEET 1 AA5 4 GLN H 4 SER H 8 0 SHEET 2 AA5 4 LEU H 19 SER H 26 -1 O SER H 22 N SER H 8 SHEET 3 AA5 4 SER H 79 MET H 84 -1 O MET H 84 N LEU H 19 SHEET 4 AA5 4 PHE H 69 ASP H 74 -1 N THR H 70 O GLN H 83 SHEET 1 AA6 6 LEU H 12 VAL H 13 0 SHEET 2 AA6 6 THR H 116 VAL H 120 1 O THR H 119 N VAL H 13 SHEET 3 AA6 6 ALA H 93 GLU H 100 -1 N ALA H 93 O VAL H 118 SHEET 4 AA6 6 TRP H 34 GLN H 40 -1 N VAL H 38 O TYR H 96 SHEET 5 AA6 6 LEU H 46 ILE H 52 -1 O GLU H 47 N ARG H 39 SHEET 6 AA6 6 LYS H 59 TYR H 61 -1 O TYR H 60 N ASN H 51 SHEET 1 AA7 4 LEU H 12 VAL H 13 0 SHEET 2 AA7 4 THR H 116 VAL H 120 1 O THR H 119 N VAL H 13 SHEET 3 AA7 4 ALA H 93 GLU H 100 -1 N ALA H 93 O VAL H 118 SHEET 4 AA7 4 TYR H 111 TRP H 112 -1 O TYR H 111 N ARG H 99 SHEET 1 AA8 4 LEU L 4 SER L 7 0 SHEET 2 AA8 4 ALA L 19 ALA L 25 -1 O SER L 22 N SER L 7 SHEET 3 AA8 4 ASP L 71 ILE L 76 -1 O LEU L 74 N LEU L 21 SHEET 4 AA8 4 PHE L 63 SER L 68 -1 N SER L 64 O THR L 75 SHEET 1 AA9 6 THR L 10 LEU L 13 0 SHEET 2 AA9 6 THR L 103 ILE L 107 1 O LYS L 104 N LEU L 11 SHEET 3 AA9 6 ALA L 85 GLN L 91 -1 N ALA L 85 O VAL L 105 SHEET 4 AA9 6 LEU L 34 GLN L 39 -1 N ALA L 35 O GLN L 90 SHEET 5 AA9 6 ARG L 46 TYR L 50 -1 O LEU L 48 N TRP L 36 SHEET 6 AA9 6 SER L 54 ARG L 55 -1 O SER L 54 N TYR L 50 SHEET 1 AB1 4 THR L 10 LEU L 13 0 SHEET 2 AB1 4 THR L 103 ILE L 107 1 O LYS L 104 N LEU L 11 SHEET 3 AB1 4 ALA L 85 GLN L 91 -1 N ALA L 85 O VAL L 105 SHEET 4 AB1 4 THR L 98 PHE L 99 -1 O THR L 98 N GLN L 91 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.03 SSBOND 2 CYS A 155 CYS A 209 1555 1555 2.03 SSBOND 3 CYS H 23 CYS H 97 1555 1555 2.04 SSBOND 4 CYS L 23 CYS L 89 1555 1555 2.05 CISPEP 1 TYR A 160 PRO A 161 0 -4.88 CISPEP 2 SER H 8 GLY H 9 0 -15.40 CISPEP 3 SER L 7 PRO L 8 0 -4.46 CISPEP 4 LEU L 95 PRO L 96 0 -0.29 CRYST1 133.890 133.890 133.890 90.00 90.00 90.00 P 2 3 12 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 0.007469 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007469 0.00000