HEADER IMMUNE SYSTEM 04-MAR-21 7E9B TITLE STRUCTURAL BASIS OF HLX10 PD-1 RECEPTOR RECOGNITION, A PROMISING ANTI- TITLE 2 PD-1 ANTIBODY CLINICAL CANDIDATE FOR CANCER IMMUNOTHERAPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF FAB FRAGMENT OF HLX10; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF FAB FRAGMENT OF HLX10; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 11 CHAIN: C; COMPND 12 SYNONYM: PROTEIN PD-1,HPD-1; 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 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: PDCD1, PD1; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECSZW-2; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 2419741 KEYWDS ANTIBODY, MAB, PD-1, PD-L-1, CANCER, T-CELL, IMMUNOTHERAPY, ICI, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.L.FAN,W.D.JIANG REVDAT 3 29-NOV-23 7E9B 1 REMARK REVDAT 2 16-FEB-22 7E9B 1 JRNL REVDAT 1 28-JUL-21 7E9B 0 JRNL AUTH H.ISSAFRAS,S.FAN,C.L.TSENG,Y.CHENG,P.LIN,L.XIAO,Y.J.HUANG, JRNL AUTH 2 C.H.TU,Y.C.HSIAO,M.LI,Y.H.CHEN,C.H.HO,O.LI,Y.WANG,S.CHEN, JRNL AUTH 3 Z.JI,E.ZHANG,Y.T.MAO,E.LIU,S.YANG,W.JIANG JRNL TITL STRUCTURAL BASIS OF HLX10 PD-1 RECEPTOR RECOGNITION, A JRNL TITL 2 PROMISING ANTI-PD-1 ANTIBODY CLINICAL CANDIDATE FOR CANCER JRNL TITL 3 IMMUNOTHERAPY. JRNL REF PLOS ONE V. 16 57972 2021 JRNL REFN ESSN 1932-6203 JRNL PMID 34972111 JRNL DOI 10.1371/JOURNAL.PONE.0257972 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3855 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 48174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 31.4100 - 4.2800 0.92 3216 140 0.1568 0.1864 REMARK 3 2 4.2800 - 3.4000 0.96 3367 146 0.1519 0.1792 REMARK 3 3 3.4000 - 2.9700 0.92 3215 138 0.1698 0.1993 REMARK 3 4 2.9700 - 2.7000 0.96 3351 147 0.1838 0.2420 REMARK 3 5 2.7000 - 2.5100 0.97 3357 145 0.1807 0.2472 REMARK 3 6 2.5100 - 2.3600 0.92 3209 139 0.1813 0.2413 REMARK 3 7 2.3600 - 2.2400 0.96 3349 144 0.1760 0.2108 REMARK 3 8 2.2400 - 2.1400 0.96 3329 144 0.1769 0.2217 REMARK 3 9 2.1400 - 2.0600 0.97 3351 146 0.1761 0.2184 REMARK 3 10 2.0600 - 1.9900 0.93 3278 141 0.1757 0.2398 REMARK 3 11 1.9900 - 1.9300 0.96 3347 146 0.1729 0.2328 REMARK 3 12 1.9300 - 1.8700 0.96 3311 143 0.1842 0.2232 REMARK 3 13 1.8700 - 1.8200 0.96 3421 147 0.2009 0.2210 REMARK 3 14 1.8200 - 1.7800 0.90 3074 133 0.2287 0.3096 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.72 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 : 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 : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 1 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.2097 12.9926 -25.8674 REMARK 3 T TENSOR REMARK 3 T11: 0.1461 T22: 0.1710 REMARK 3 T33: 0.1710 T12: 0.0135 REMARK 3 T13: 0.0218 T23: 0.0440 REMARK 3 L TENSOR REMARK 3 L11: 1.2075 L22: 3.3804 REMARK 3 L33: 2.1077 L12: 0.6899 REMARK 3 L13: 0.6065 L23: 1.1796 REMARK 3 S TENSOR REMARK 3 S11: -0.0535 S12: 0.0823 S13: 0.1496 REMARK 3 S21: -0.1320 S22: 0.0057 S23: -0.0611 REMARK 3 S31: -0.1526 S32: 0.0540 S33: 0.0594 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 113 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1674 19.3052 1.1502 REMARK 3 T TENSOR REMARK 3 T11: 0.2320 T22: 0.1893 REMARK 3 T33: 0.2097 T12: -0.0127 REMARK 3 T13: -0.0008 T23: 0.0393 REMARK 3 L TENSOR REMARK 3 L11: 2.2725 L22: 1.0242 REMARK 3 L33: 2.0664 L12: -0.4485 REMARK 3 L13: 1.1053 L23: 0.1008 REMARK 3 S TENSOR REMARK 3 S11: -0.0841 S12: -0.1412 S13: 0.0335 REMARK 3 S21: 0.1782 S22: 0.0051 S23: -0.0976 REMARK 3 S31: -0.0001 S32: 0.0583 S33: 0.0551 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 179 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6200 16.9577 4.9688 REMARK 3 T TENSOR REMARK 3 T11: 0.2836 T22: 0.2292 REMARK 3 T33: 0.3449 T12: 0.0207 REMARK 3 T13: -0.0418 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 5.8987 L22: 5.5599 REMARK 3 L33: 4.6410 L12: -1.5114 REMARK 3 L13: 0.9815 L23: -2.7562 REMARK 3 S TENSOR REMARK 3 S11: 0.0603 S12: -0.1448 S13: 0.3610 REMARK 3 S21: 0.2054 S22: -0.3239 S23: -0.9265 REMARK 3 S31: 0.0906 S32: 0.5500 S33: 0.2719 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.1878 -0.4636 -4.4121 REMARK 3 T TENSOR REMARK 3 T11: 0.2589 T22: 0.3271 REMARK 3 T33: 0.1956 T12: -0.0153 REMARK 3 T13: 0.0648 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 8.6960 L22: 7.4003 REMARK 3 L33: 4.4377 L12: -5.7649 REMARK 3 L13: 4.8869 L23: -3.3229 REMARK 3 S TENSOR REMARK 3 S11: 0.0410 S12: -0.1827 S13: -0.0777 REMARK 3 S21: 0.3404 S22: 0.0105 S23: 0.2481 REMARK 3 S31: 0.0360 S32: -0.5038 S33: -0.0857 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 19 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1464 -2.3948 -13.8483 REMARK 3 T TENSOR REMARK 3 T11: 0.1198 T22: 0.1985 REMARK 3 T33: 0.1796 T12: -0.0011 REMARK 3 T13: 0.0310 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 0.4914 L22: 2.1162 REMARK 3 L33: 2.5646 L12: 0.0070 REMARK 3 L13: 0.4470 L23: -0.6103 REMARK 3 S TENSOR REMARK 3 S11: 0.0196 S12: -0.0302 S13: -0.0144 REMARK 3 S21: 0.1187 S22: -0.0178 S23: 0.0704 REMARK 3 S31: 0.0456 S32: -0.2025 S33: -0.0005 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 102 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4161 -0.7213 6.6746 REMARK 3 T TENSOR REMARK 3 T11: 0.3329 T22: 0.2289 REMARK 3 T33: 0.1860 T12: -0.0531 REMARK 3 T13: 0.0203 T23: 0.0217 REMARK 3 L TENSOR REMARK 3 L11: 2.8796 L22: 0.1685 REMARK 3 L33: 8.9966 L12: 0.4837 REMARK 3 L13: 4.6731 L23: 1.0932 REMARK 3 S TENSOR REMARK 3 S11: 0.0994 S12: -0.1015 S13: 0.0077 REMARK 3 S21: 0.3095 S22: -0.1274 S23: 0.1607 REMARK 3 S31: -0.0688 S32: 0.2935 S33: -0.0949 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 114 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4327 25.2085 13.1476 REMARK 3 T TENSOR REMARK 3 T11: 0.3757 T22: 0.3153 REMARK 3 T33: 0.3025 T12: -0.0141 REMARK 3 T13: -0.0150 T23: -0.0494 REMARK 3 L TENSOR REMARK 3 L11: 1.9497 L22: 2.1266 REMARK 3 L33: 2.6833 L12: 1.6404 REMARK 3 L13: -0.6342 L23: -1.1971 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: 0.0669 S13: -0.0567 REMARK 3 S21: 0.0637 S22: 0.0460 S23: -0.6651 REMARK 3 S31: -0.0398 S32: 0.4445 S33: -0.1511 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 129 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1596 15.1485 12.7260 REMARK 3 T TENSOR REMARK 3 T11: 0.4400 T22: 0.2746 REMARK 3 T33: 0.1986 T12: -0.0294 REMARK 3 T13: -0.0843 T23: 0.0353 REMARK 3 L TENSOR REMARK 3 L11: 0.9632 L22: 7.7723 REMARK 3 L33: 0.9412 L12: 1.1013 REMARK 3 L13: -0.4774 L23: 0.3919 REMARK 3 S TENSOR REMARK 3 S11: -0.2909 S12: 0.0328 S13: -0.0260 REMARK 3 S21: -0.0633 S22: 0.2480 S23: 0.2276 REMARK 3 S31: -0.0031 S32: -0.1856 S33: -0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 151 THROUGH 174 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.0190 13.4697 8.8288 REMARK 3 T TENSOR REMARK 3 T11: 0.1689 T22: 0.2246 REMARK 3 T33: 0.1726 T12: -0.0288 REMARK 3 T13: -0.0592 T23: 0.0319 REMARK 3 L TENSOR REMARK 3 L11: 0.8680 L22: 5.4328 REMARK 3 L33: 4.0832 L12: -0.2517 REMARK 3 L13: 0.1046 L23: 1.1521 REMARK 3 S TENSOR REMARK 3 S11: 0.0459 S12: -0.0386 S13: 0.0217 REMARK 3 S21: -0.3592 S22: 0.0457 S23: -0.2207 REMARK 3 S31: 0.0757 S32: -0.1512 S33: 0.0067 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 175 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2814 22.8062 18.1043 REMARK 3 T TENSOR REMARK 3 T11: 0.3134 T22: 0.2592 REMARK 3 T33: 0.1929 T12: 0.0190 REMARK 3 T13: -0.0241 T23: -0.0239 REMARK 3 L TENSOR REMARK 3 L11: 1.4106 L22: 7.3232 REMARK 3 L33: 3.7513 L12: 1.7923 REMARK 3 L13: -0.2503 L23: 0.1726 REMARK 3 S TENSOR REMARK 3 S11: 0.1327 S12: -0.0525 S13: 0.1262 REMARK 3 S21: 0.1453 S22: -0.0802 S23: 0.2043 REMARK 3 S31: -0.2739 S32: -0.1784 S33: -0.0760 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 32 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.7360 -12.9152 -39.2596 REMARK 3 T TENSOR REMARK 3 T11: 0.2262 T22: 0.2534 REMARK 3 T33: 0.1927 T12: -0.0150 REMARK 3 T13: -0.0043 T23: 0.0334 REMARK 3 L TENSOR REMARK 3 L11: 4.0602 L22: 2.9324 REMARK 3 L33: 4.2536 L12: -0.1223 REMARK 3 L13: -0.1555 L23: 2.3986 REMARK 3 S TENSOR REMARK 3 S11: 0.1670 S12: -0.3511 S13: 0.1840 REMARK 3 S21: 0.0601 S22: -0.2270 S23: 0.3226 REMARK 3 S31: 0.1283 S32: -0.2468 S33: 0.0555 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 83 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.0277 -10.2177 -40.9943 REMARK 3 T TENSOR REMARK 3 T11: 0.2525 T22: 0.2355 REMARK 3 T33: 0.2393 T12: 0.0257 REMARK 3 T13: 0.0491 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 1.9126 L22: 6.3776 REMARK 3 L33: 5.6214 L12: 2.5756 REMARK 3 L13: 1.0255 L23: 5.3261 REMARK 3 S TENSOR REMARK 3 S11: -0.0410 S12: -0.0604 S13: -0.1924 REMARK 3 S21: 0.0340 S22: 0.3069 S23: -0.3724 REMARK 3 S31: 0.2579 S32: 0.2098 S33: -0.2781 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 111 THROUGH 146 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.2641 -16.5747 -37.7879 REMARK 3 T TENSOR REMARK 3 T11: 0.2075 T22: 0.2360 REMARK 3 T33: 0.2090 T12: -0.0198 REMARK 3 T13: 0.0058 T23: 0.0549 REMARK 3 L TENSOR REMARK 3 L11: 1.6729 L22: 5.1393 REMARK 3 L33: 3.2294 L12: 0.4850 REMARK 3 L13: 0.6282 L23: 2.4977 REMARK 3 S TENSOR REMARK 3 S11: 0.0151 S12: -0.1164 S13: -0.2644 REMARK 3 S21: 0.2127 S22: -0.1583 S23: 0.3856 REMARK 3 S31: 0.3950 S32: -0.1801 S33: 0.1690 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 7E9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9751 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48174 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.779 REMARK 200 RESOLUTION RANGE LOW (A) : 31.414 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 4ZQK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7.5 CONTAINING 23% (W/V) REMARK 280 PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 CYS H 130 REMARK 465 SER H 131 REMARK 465 ARG H 132 REMARK 465 SER H 133 REMARK 465 THR H 134 REMARK 465 SER H 135 REMARK 465 GLU L 213 REMARK 465 CYS L 214 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 H 136 CG CD 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 H 493 O HOH H 494 1.88 REMARK 500 O HOH L 358 O HOH L 412 1.90 REMARK 500 O HOH H 477 O HOH H 488 1.93 REMARK 500 N TRP C 32 O HOH C 201 1.95 REMARK 500 O HOH L 314 O HOH L 453 1.99 REMARK 500 O HOH L 348 O HOH L 485 2.03 REMARK 500 O HOH L 448 O HOH L 493 2.03 REMARK 500 NE ARG L 18 O HOH L 301 2.03 REMARK 500 OD1 ASP L 1 O HOH L 302 2.04 REMARK 500 O HOH H 452 O HOH L 480 2.04 REMARK 500 O HOH H 463 O HOH L 406 2.04 REMARK 500 O HOH C 232 O HOH C 284 2.06 REMARK 500 O HOH H 406 O HOH H 482 2.08 REMARK 500 O HOH L 335 O HOH L 364 2.12 REMARK 500 OG1 THR C 59 O HOH C 202 2.14 REMARK 500 O GLN C 88 O HOH C 203 2.15 REMARK 500 OG SER H 56 OE1 GLU C 61 2.15 REMARK 500 O HOH H 425 O HOH H 449 2.16 REMARK 500 O HOH H 431 O HOH H 482 2.16 REMARK 500 OE2 GLU H 215 O HOH H 301 2.16 REMARK 500 O HOH L 348 O HOH C 277 2.17 REMARK 500 O GLY L 212 O HOH L 303 2.17 REMARK 500 OD2 ASP H 104 O HOH H 302 2.17 REMARK 500 O HOH L 462 O HOH L 480 2.18 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 TYR H 100 -99.87 -149.49 REMARK 500 THR L 30 -117.70 52.02 REMARK 500 ALA L 51 -40.47 73.10 REMARK 500 ALA L 84 179.70 178.05 REMARK 500 ASN L 152 -15.21 78.31 REMARK 500 SER L 156 -72.29 -117.73 REMARK 500 SER C 62 53.15 -90.08 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 H 495 DISTANCE = 6.35 ANGSTROMS DBREF 7E9B H 1 215 PDB 7E9B 7E9B 1 215 DBREF 7E9B L 1 214 PDB 7E9B 7E9B 1 214 DBREF 7E9B C 32 146 UNP Q15116 PDCD1_HUMAN 32 146 SEQRES 1 H 215 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL LYS SEQRES 2 H 215 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 215 PHE THR PHE SER ASN TYR GLY MET SER TRP ILE ARG GLN SEQRES 4 H 215 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER THR ILE SER SEQRES 5 H 215 GLY GLY GLY SER ASN ILE TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 215 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 215 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 215 ALA VAL TYR TYR CYS VAL SER TYR TYR TYR GLY ILE ASP SEQRES 9 H 215 PHE TRP GLY GLN GLY THR SER VAL THR VAL SER SER ALA SEQRES 10 H 215 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO CYS SEQRES 11 H 215 SER ARG SER THR SER GLU SER THR ALA ALA LEU GLY CYS SEQRES 12 H 215 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER SEQRES 13 H 215 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE SEQRES 14 H 215 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SEQRES 15 H 215 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR LYS SEQRES 16 H 215 THR TYR THR CYS ASN VAL ASP HIS LYS PRO SER ASN THR SEQRES 17 H 215 LYS VAL ASP LYS ARG VAL GLU SEQRES 1 L 214 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS LYS ALA SER SEQRES 3 L 214 GLN ASP VAL THR THR ALA VAL ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR TRP ALA SER SEQRES 5 L 214 THR ARG HIS THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN HIS SEQRES 8 L 214 TYR THR ILE PRO TRP THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS SEQRES 1 C 115 TRP ASN PRO PRO THR PHE SER PRO ALA LEU LEU VAL VAL SEQRES 2 C 115 THR GLU GLY ASP ASN ALA THR PHE THR CYS SER PHE SER SEQRES 3 C 115 ASN THR SER GLU SER PHE VAL LEU ASN TRP TYR ARG MET SEQRES 4 C 115 SER PRO SER ASN GLN THR ASP LYS LEU ALA ALA PHE PRO SEQRES 5 C 115 GLU ASP ARG SER GLN PRO GLY GLN ASP CYS ARG PHE ARG SEQRES 6 C 115 VAL THR GLN LEU PRO ASN GLY ARG ASP PHE HIS MET SER SEQRES 7 C 115 VAL VAL ARG ALA ARG ARG ASN ASP SER GLY THR TYR LEU SEQRES 8 C 115 CYS GLY ALA ILE SER LEU ALA PRO LYS ALA GLN ILE LYS SEQRES 9 C 115 GLU SER LEU ARG ALA GLU LEU ARG VAL THR GLU FORMUL 4 HOH *489(H2 O) HELIX 1 AA1 THR H 28 TYR H 32 5 5 HELIX 2 AA2 ARG H 87 THR H 91 5 5 HELIX 3 AA3 SER H 159 ALA H 161 5 3 HELIX 4 AA4 SER H 190 THR H 194 5 5 HELIX 5 AA5 LYS H 204 ASN H 207 5 4 HELIX 6 AA6 GLN L 79 PHE L 83 5 5 HELIX 7 AA7 SER L 121 SER L 127 1 7 HELIX 8 AA8 LYS L 183 LYS L 188 1 6 HELIX 9 AA9 ARG C 114 SER C 118 5 5 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA1 4 SER H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA1 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA2 6 LEU H 11 VAL H 12 0 SHEET 2 AA2 6 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AA2 6 ALA H 92 SER H 98 -1 N TYR H 94 O THR H 110 SHEET 4 AA2 6 MET H 34 GLN H 39 -1 N ILE H 37 O TYR H 95 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 ILE H 58 TYR H 60 -1 O TYR H 59 N THR H 50 SHEET 1 AA3 4 LEU H 11 VAL H 12 0 SHEET 2 AA3 4 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AA3 4 ALA H 92 SER H 98 -1 N TYR H 94 O THR H 110 SHEET 4 AA3 4 PHE H 105 TRP H 106 -1 O PHE H 105 N SER H 98 SHEET 1 AA4 4 SER H 123 LEU H 127 0 SHEET 2 AA4 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 AA4 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148 SHEET 4 AA4 4 VAL H 166 THR H 168 -1 N HIS H 167 O VAL H 184 SHEET 1 AA5 4 SER H 123 LEU H 127 0 SHEET 2 AA5 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 AA5 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148 SHEET 4 AA5 4 VAL H 172 LEU H 173 -1 N VAL H 172 O SER H 180 SHEET 1 AA6 3 THR H 154 TRP H 157 0 SHEET 2 AA6 3 THR H 198 HIS H 203 -1 O ASN H 200 N SER H 156 SHEET 3 AA6 3 THR H 208 ARG H 213 -1 O VAL H 210 N VAL H 201 SHEET 1 AA7 4 MET L 4 SER L 7 0 SHEET 2 AA7 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 AA7 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 AA7 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AA8 6 SER L 10 ALA L 13 0 SHEET 2 AA8 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AA8 6 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 AA8 6 VAL L 33 GLN L 38 -1 N ALA L 34 O GLN L 89 SHEET 5 AA8 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA8 6 THR L 53 ARG L 54 -1 O THR L 53 N TYR L 49 SHEET 1 AA9 4 SER L 10 ALA L 13 0 SHEET 2 AA9 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AA9 4 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 AA9 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB1 4 SER L 114 PHE L 118 0 SHEET 2 AB1 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AB1 4 TYR L 173 SER L 182 -1 O TYR L 173 N PHE L 139 SHEET 4 AB1 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AB2 4 ALA L 153 LEU L 154 0 SHEET 2 AB2 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB2 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB2 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 AB3 4 THR C 36 SER C 38 0 SHEET 2 AB3 4 ALA C 50 SER C 55 -1 O THR C 53 N SER C 38 SHEET 3 AB3 4 ASP C 105 VAL C 110 -1 O MET C 108 N PHE C 52 SHEET 4 AB3 4 PHE C 95 GLN C 99 -1 N ARG C 96 O SER C 109 SHEET 1 AB4 5 LEU C 41 THR C 45 0 SHEET 2 AB4 5 ALA C 140 THR C 145 1 O THR C 145 N VAL C 44 SHEET 3 AB4 5 GLY C 119 SER C 127 -1 N GLY C 119 O LEU C 142 SHEET 4 AB4 5 PHE C 63 MET C 70 -1 N ASN C 66 O GLY C 124 SHEET 5 AB4 5 THR C 76 PHE C 82 -1 O LEU C 79 N TRP C 67 SHEET 1 AB5 4 LEU C 41 THR C 45 0 SHEET 2 AB5 4 ALA C 140 THR C 145 1 O THR C 145 N VAL C 44 SHEET 3 AB5 4 GLY C 119 SER C 127 -1 N GLY C 119 O LEU C 142 SHEET 4 AB5 4 GLN C 133 GLU C 136 -1 O LYS C 135 N ALA C 125 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.05 SSBOND 2 CYS H 143 CYS H 199 1555 1555 2.03 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.06 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.06 SSBOND 5 CYS C 54 CYS C 123 1555 1555 2.06 CISPEP 1 PHE H 149 PRO H 150 0 -4.86 CISPEP 2 GLU H 151 PRO H 152 0 0.14 CISPEP 3 SER L 7 PRO L 8 0 -3.00 CISPEP 4 ILE L 94 PRO L 95 0 0.02 CISPEP 5 TYR L 140 PRO L 141 0 3.09 CISPEP 6 SER C 38 PRO C 39 0 -3.24 CISPEP 7 PHE C 82 PRO C 83 0 -7.49 CISPEP 8 ALA C 129 PRO C 130 0 0.29 CRYST1 38.985 45.014 80.890 93.60 102.16 97.34 P 1 1 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 0.025651 0.003306 0.005858 0.00000 SCALE2 0.000000 0.022399 0.002082 0.00000 SCALE3 0.000000 0.000000 0.012701 0.00000