PDB Short entry for 5N2F HEADER IMMUNE SYSTEM 07-FEB-17 5N2F TITLE STRUCTURE OF PD-L1/SMALL-MOLECULE INHIBITOR COMPLEX 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: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 10 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_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PD-L1, PD-1, SMALL-MOLECULE INHIBITOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.GUZIK,K.M.ZAK,P.GRUDNIK,G.DUBIN,T.A.HOLAK REVDAT 3 17-JAN-24 5N2F 1 REMARK REVDAT 2 26-JUL-17 5N2F 1 REVDAT 1 28-JUN-17 5N2F 0 JRNL AUTH K.GUZIK,K.M.ZAK,P.GRUDNIK,K.MAGIERA,B.MUSIELAK,R.TORNER, JRNL AUTH 2 L.SKALNIAK,A.DOMLING,G.DUBIN,T.A.HOLAK JRNL TITL SMALL-MOLECULE INHIBITORS OF THE PROGRAMMED CELL JRNL TITL 2 DEATH-1/PROGRAMMED DEATH-LIGAND 1 (PD-1/PD-L1) INTERACTION JRNL TITL 3 VIA TRANSIENTLY INDUCED PROTEIN STATES AND DIMERIZATION OF JRNL TITL 4 PD-L1. JRNL REF J. MED. CHEM. V. 60 5857 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28613862 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00293 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34155 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1664 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 36.8452 - 3.8907 0.99 2910 124 0.1572 0.1882 REMARK 3 2 3.8907 - 3.0886 1.00 2754 133 0.1705 0.1933 REMARK 3 3 3.0886 - 2.6984 1.00 2712 168 0.2026 0.2344 REMARK 3 4 2.6984 - 2.4517 1.00 2694 146 0.2160 0.2769 REMARK 3 5 2.4517 - 2.2760 1.00 2685 138 0.2124 0.2488 REMARK 3 6 2.2760 - 2.1418 1.00 2702 152 0.2153 0.2559 REMARK 3 7 2.1418 - 2.0346 1.00 2681 130 0.2192 0.2597 REMARK 3 8 2.0346 - 1.9460 1.00 2659 133 0.2028 0.2393 REMARK 3 9 1.9460 - 1.8711 1.00 2674 151 0.2134 0.2656 REMARK 3 10 1.8711 - 1.8065 1.00 2649 142 0.2260 0.2568 REMARK 3 11 1.8065 - 1.7500 1.00 2652 144 0.2490 0.3267 REMARK 3 12 1.7500 - 1.7000 1.00 2719 103 0.2822 0.3451 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.500 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 : 0.009 2090 REMARK 3 ANGLE : 1.025 2852 REMARK 3 CHIRALITY : 0.059 317 REMARK 3 PLANARITY : 0.006 364 REMARK 3 DIHEDRAL : 20.407 1264 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 19 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.5649 7.1780 125.6869 REMARK 3 T TENSOR REMARK 3 T11: 0.2187 T22: 0.1789 REMARK 3 T33: 0.2204 T12: 0.0206 REMARK 3 T13: -0.0204 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.7545 L22: 1.4331 REMARK 3 L33: 2.5330 L12: 1.2083 REMARK 3 L13: 0.8129 L23: 1.3084 REMARK 3 S TENSOR REMARK 3 S11: 0.1438 S12: -0.1335 S13: -0.1295 REMARK 3 S21: 0.1598 S22: -0.0333 S23: -0.0894 REMARK 3 S31: 0.0842 S32: -0.2512 S33: -0.1474 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 36 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9663 15.9150 135.5387 REMARK 3 T TENSOR REMARK 3 T11: 0.2843 T22: 0.2031 REMARK 3 T33: 0.2568 T12: 0.0350 REMARK 3 T13: 0.0480 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 2.4578 L22: 2.0343 REMARK 3 L33: 3.1571 L12: -0.2281 REMARK 3 L13: 0.4601 L23: 1.0126 REMARK 3 S TENSOR REMARK 3 S11: 0.1951 S12: -0.1651 S13: 0.1003 REMARK 3 S21: 0.2078 S22: -0.0521 S23: 0.1451 REMARK 3 S31: 0.2140 S32: -0.0133 S33: -0.1111 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5855 18.9991 125.7383 REMARK 3 T TENSOR REMARK 3 T11: 0.2582 T22: 0.2296 REMARK 3 T33: 0.2980 T12: 0.0167 REMARK 3 T13: 0.0091 T23: -0.0495 REMARK 3 L TENSOR REMARK 3 L11: 5.2168 L22: 4.6978 REMARK 3 L33: 3.1090 L12: 1.9151 REMARK 3 L13: 1.0488 L23: 0.2033 REMARK 3 S TENSOR REMARK 3 S11: 0.0817 S12: 0.5649 S13: 0.0069 REMARK 3 S21: -0.1045 S22: 0.3948 S23: -0.6349 REMARK 3 S31: -0.3778 S32: 0.6518 S33: -0.4834 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5747 26.0349 122.8329 REMARK 3 T TENSOR REMARK 3 T11: 1.0363 T22: 0.3516 REMARK 3 T33: 0.4576 T12: -0.1045 REMARK 3 T13: -0.0758 T23: 0.0624 REMARK 3 L TENSOR REMARK 3 L11: 7.5926 L22: 3.1500 REMARK 3 L33: 5.0106 L12: 0.3154 REMARK 3 L13: -0.4926 L23: 3.9347 REMARK 3 S TENSOR REMARK 3 S11: -0.3777 S12: 0.7352 S13: 1.6766 REMARK 3 S21: -0.2081 S22: 0.7689 S23: -0.4947 REMARK 3 S31: -1.6497 S32: 0.2945 S33: -0.4505 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1527 19.9995 114.0609 REMARK 3 T TENSOR REMARK 3 T11: 0.5523 T22: 0.7135 REMARK 3 T33: 0.2569 T12: -0.0591 REMARK 3 T13: -0.0673 T23: 0.0908 REMARK 3 L TENSOR REMARK 3 L11: 6.9038 L22: 7.9079 REMARK 3 L33: 1.4705 L12: 3.1498 REMARK 3 L13: -2.7856 L23: 0.2249 REMARK 3 S TENSOR REMARK 3 S11: -0.0748 S12: 1.0759 S13: 0.7133 REMARK 3 S21: -1.1907 S22: -0.0106 S23: 0.3309 REMARK 3 S31: -1.0044 S32: 1.1334 S33: -0.0345 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 85 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8882 20.6021 130.7039 REMARK 3 T TENSOR REMARK 3 T11: 0.3725 T22: 0.3581 REMARK 3 T33: 0.3492 T12: 0.0952 REMARK 3 T13: -0.0226 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 3.2556 L22: 1.0237 REMARK 3 L33: 2.6991 L12: -0.3326 REMARK 3 L13: -2.1450 L23: 1.3500 REMARK 3 S TENSOR REMARK 3 S11: 0.2275 S12: 0.1046 S13: -0.0186 REMARK 3 S21: 0.0516 S22: -0.0458 S23: 0.5034 REMARK 3 S31: -1.3526 S32: -1.2466 S33: -0.0057 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6840 13.5789 118.7482 REMARK 3 T TENSOR REMARK 3 T11: 0.2359 T22: 0.2378 REMARK 3 T33: 0.2480 T12: 0.0197 REMARK 3 T13: -0.0110 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 2.2969 L22: 0.9958 REMARK 3 L33: 4.4093 L12: 1.3090 REMARK 3 L13: 2.8539 L23: 2.0748 REMARK 3 S TENSOR REMARK 3 S11: -0.2019 S12: 0.1177 S13: 0.0393 REMARK 3 S21: -0.1063 S22: 0.0301 S23: 0.0013 REMARK 3 S31: -0.4512 S32: 0.2042 S33: 0.0722 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 110 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.7913 13.3338 129.1942 REMARK 3 T TENSOR REMARK 3 T11: 0.2662 T22: 0.2244 REMARK 3 T33: 0.2894 T12: 0.0395 REMARK 3 T13: -0.0406 T23: -0.1071 REMARK 3 L TENSOR REMARK 3 L11: 2.0171 L22: 3.0751 REMARK 3 L33: 8.8998 L12: 1.8220 REMARK 3 L13: 2.9014 L23: 5.0860 REMARK 3 S TENSOR REMARK 3 S11: -0.0588 S12: 0.0482 S13: 0.0579 REMARK 3 S21: 0.2291 S22: 0.1287 S23: -0.0725 REMARK 3 S31: 0.0526 S32: 0.1899 S33: -0.2751 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 120 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.1472 6.5785 125.3260 REMARK 3 T TENSOR REMARK 3 T11: 0.2341 T22: 0.1739 REMARK 3 T33: 0.2321 T12: 0.0550 REMARK 3 T13: -0.0274 T23: -0.0519 REMARK 3 L TENSOR REMARK 3 L11: 5.6289 L22: 3.5849 REMARK 3 L33: 1.6754 L12: 3.4604 REMARK 3 L13: 2.1537 L23: 2.4684 REMARK 3 S TENSOR REMARK 3 S11: -0.0190 S12: 0.3127 S13: -0.3605 REMARK 3 S21: 0.1844 S22: 0.3495 S23: -0.3129 REMARK 3 S31: 0.0232 S32: 0.4972 S33: -0.4764 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0178 5.6153 101.2903 REMARK 3 T TENSOR REMARK 3 T11: 0.3458 T22: 0.3251 REMARK 3 T33: 0.3530 T12: -0.0255 REMARK 3 T13: 0.0449 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 3.9158 L22: 4.1332 REMARK 3 L33: 6.8108 L12: 3.9089 REMARK 3 L13: -0.6314 L23: 0.0003 REMARK 3 S TENSOR REMARK 3 S11: -0.2633 S12: 0.2980 S13: 0.2207 REMARK 3 S21: -0.5817 S22: -0.0162 S23: -0.7314 REMARK 3 S31: -0.6781 S32: 0.3945 S33: 0.2864 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.4389 11.6650 122.5388 REMARK 3 T TENSOR REMARK 3 T11: 0.2196 T22: 0.2253 REMARK 3 T33: 0.2404 T12: -0.0103 REMARK 3 T13: -0.0031 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 1.9417 L22: 1.5540 REMARK 3 L33: 2.3735 L12: -0.3421 REMARK 3 L13: -1.5188 L23: 1.6175 REMARK 3 S TENSOR REMARK 3 S11: 0.1176 S12: -0.0629 S13: 0.3504 REMARK 3 S21: -0.0889 S22: 0.0556 S23: -0.2044 REMARK 3 S31: -0.1845 S32: 0.0511 S33: -0.1509 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 39 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.5620 22.4687 134.1875 REMARK 3 T TENSOR REMARK 3 T11: 0.6125 T22: 0.3264 REMARK 3 T33: 0.5173 T12: -0.0095 REMARK 3 T13: -0.1160 T23: -0.1434 REMARK 3 L TENSOR REMARK 3 L11: 0.6705 L22: 3.3762 REMARK 3 L33: 3.6576 L12: 0.0343 REMARK 3 L13: 0.0837 L23: 1.2179 REMARK 3 S TENSOR REMARK 3 S11: -0.0417 S12: -0.3872 S13: 0.2434 REMARK 3 S21: 0.8658 S22: -0.1900 S23: -0.3840 REMARK 3 S31: -0.8950 S32: -0.0050 S33: -0.1538 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 50 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.9437 9.2192 132.8290 REMARK 3 T TENSOR REMARK 3 T11: 0.2347 T22: 0.2836 REMARK 3 T33: 0.1974 T12: -0.0072 REMARK 3 T13: -0.0154 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 5.5387 L22: 4.6612 REMARK 3 L33: 3.6058 L12: -1.4107 REMARK 3 L13: -1.4713 L23: 1.8079 REMARK 3 S TENSOR REMARK 3 S11: 0.0600 S12: -0.4217 S13: -0.1994 REMARK 3 S21: 0.4478 S22: 0.0617 S23: 0.1332 REMARK 3 S31: 0.0566 S32: -0.5346 S33: 0.0083 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 69 THROUGH 81 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.1436 3.0447 137.3715 REMARK 3 T TENSOR REMARK 3 T11: 0.3199 T22: 0.2701 REMARK 3 T33: 0.3654 T12: -0.0465 REMARK 3 T13: -0.0133 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 3.6308 L22: 5.4831 REMARK 3 L33: 3.1264 L12: 0.6325 REMARK 3 L13: 0.1690 L23: -4.0681 REMARK 3 S TENSOR REMARK 3 S11: -0.1497 S12: -0.4778 S13: -0.1912 REMARK 3 S21: 0.6685 S22: -0.2870 S23: -0.1089 REMARK 3 S31: -0.2581 S32: -0.3403 S33: 0.3876 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 82 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.5964 2.7592 134.6280 REMARK 3 T TENSOR REMARK 3 T11: 0.3374 T22: 0.3587 REMARK 3 T33: 0.3573 T12: 0.0275 REMARK 3 T13: 0.0014 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 5.2527 L22: 3.0235 REMARK 3 L33: 2.7903 L12: -3.9400 REMARK 3 L13: 0.2619 L23: -0.6303 REMARK 3 S TENSOR REMARK 3 S11: -0.1297 S12: -0.7900 S13: -0.5486 REMARK 3 S21: 0.8954 S22: 0.2962 S23: -0.6557 REMARK 3 S31: 0.4575 S32: 0.3192 S33: 0.0730 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 89 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.9026 18.0865 135.9010 REMARK 3 T TENSOR REMARK 3 T11: 0.4277 T22: 0.3869 REMARK 3 T33: 0.7335 T12: -0.0227 REMARK 3 T13: -0.2007 T23: -0.1597 REMARK 3 L TENSOR REMARK 3 L11: 4.1763 L22: 4.7098 REMARK 3 L33: 2.2522 L12: 4.3977 REMARK 3 L13: -0.8696 L23: -0.5140 REMARK 3 S TENSOR REMARK 3 S11: -0.3787 S12: -1.0520 S13: 0.6354 REMARK 3 S21: 1.0048 S22: -0.2397 S23: -2.0579 REMARK 3 S31: -0.3699 S32: 0.2661 S33: 0.4544 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 99 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.4081 8.0656 127.0223 REMARK 3 T TENSOR REMARK 3 T11: 0.1508 T22: 0.2167 REMARK 3 T33: 0.1397 T12: -0.0174 REMARK 3 T13: 0.0029 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 4.3360 L22: 4.8573 REMARK 3 L33: 3.0398 L12: -1.6995 REMARK 3 L13: -0.1735 L23: 1.5426 REMARK 3 S TENSOR REMARK 3 S11: -0.0150 S12: -0.2332 S13: -0.0311 REMARK 3 S21: 0.2084 S22: -0.0679 S23: 0.0351 REMARK 3 S31: -0.0680 S32: -0.1397 S33: 0.0899 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 120 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.4521 12.0207 121.2676 REMARK 3 T TENSOR REMARK 3 T11: 0.2211 T22: 0.2267 REMARK 3 T33: 0.1959 T12: -0.0005 REMARK 3 T13: -0.0014 T23: -0.0480 REMARK 3 L TENSOR REMARK 3 L11: 8.3733 L22: 4.4660 REMARK 3 L33: 6.1651 L12: -5.8961 REMARK 3 L13: -5.9250 L23: 4.8365 REMARK 3 S TENSOR REMARK 3 S11: 0.2397 S12: 0.3354 S13: 0.1833 REMARK 3 S21: -0.0633 S22: -0.3653 S23: -0.0083 REMARK 3 S31: -0.2307 S32: -0.4642 S33: 0.3374 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 132 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.4161 -10.8137 114.2982 REMARK 3 T TENSOR REMARK 3 T11: 0.2788 T22: 0.2733 REMARK 3 T33: 0.2826 T12: -0.0236 REMARK 3 T13: 0.0043 T23: 0.0854 REMARK 3 L TENSOR REMARK 3 L11: 1.7366 L22: 3.1123 REMARK 3 L33: 8.2831 L12: 0.9252 REMARK 3 L13: 2.1117 L23: 3.6718 REMARK 3 S TENSOR REMARK 3 S11: -0.0977 S12: -0.5735 S13: -0.2368 REMARK 3 S21: 0.6975 S22: 0.5473 S23: 0.0006 REMARK 3 S31: 0.8868 S32: -1.0313 S33: -0.3354 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 5N2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003455. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 36.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.50200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 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 (%): 53.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M TRIS PH 8.4 , 0.28 M SODIUM REMARK 280 CHLORIDE, 27% (W/V) PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 26.18950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.76300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.18950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.76300 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: 1270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 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 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 GLU B 72 CG CD OE1 OE2 REMARK 470 LYS B 89 CD CE NZ REMARK 470 GLN B 91 CG CD OE1 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 CYS B 40 N CA C O CB SG 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 NE2 GLN A 107 O HOH A 201 1.99 REMARK 500 O HOH B 353 O HOH B 419 2.03 REMARK 500 O ALA B 51 O HOH B 301 2.04 REMARK 500 O HOH B 364 O HOH B 398 2.04 REMARK 500 O HOH B 417 O HOH B 425 2.08 REMARK 500 NE2 GLN B 107 O HOH B 302 2.10 REMARK 500 O HOH B 336 O HOH B 385 2.18 REMARK 500 O HOH B 394 O HOH B 405 2.18 REMARK 500 NH1 ARG A 113 OD1 ASP B 61 2.19 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 114 CB CYS A 114 SG -0.194 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 -36.81 70.00 REMARK 500 LYS A 75 44.65 -106.63 REMARK 500 TYR A 118 82.42 -153.96 REMARK 500 GLU B 45 -77.83 -85.38 REMARK 500 HIS B 69 -87.47 45.32 REMARK 500 GLU B 71 -158.53 -157.63 REMARK 500 GLN B 83 10.28 59.93 REMARK 500 ALA B 97 50.37 -110.78 REMARK 500 ASP B 103 70.18 61.17 REMARK 500 TYR B 118 92.17 -166.34 REMARK 500 TYR B 118 84.92 -166.34 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 326 DISTANCE = 6.01 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8HW B 201 DBREF 5N2F A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 5N2F B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 SEQADV 5N2F ALA A 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F ALA A 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F ALA A 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F LEU A 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F GLU A 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F HIS A 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F HIS A 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F HIS A 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F HIS A 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F ALA B 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F ALA B 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F ALA B 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F LEU B 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F GLU B 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F HIS B 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5N2F HIS B 141 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 126 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 126 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 126 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 126 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 126 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 A 126 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 126 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 126 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 126 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 A 126 ALA ALA ALA LEU GLU HIS HIS HIS HIS SEQRES 1 B 124 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 B 124 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 B 124 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 B 124 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 B 124 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 B 124 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 B 124 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 B 124 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 B 124 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 B 124 ALA ALA ALA LEU GLU HIS HIS HET 8HW B 201 36 HETNAM 8HW 4-[[4-[[3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-2-METHYL- HETNAM 2 8HW PHENYL]METHOXY]-2,5-BIS(FLUORANYL)PHENYL]METHYLAMINO]- HETNAM 3 8HW 3-OXIDANYLIDENE-BUTANOIC ACID FORMUL 3 8HW C27 H25 F2 N O6 FORMUL 4 HOH *271(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 PRO A 133 HIS A 143 1 11 HELIX 6 AA6 ASP B 49 ALA B 52 5 4 HELIX 7 AA7 ASP B 73 GLN B 77 5 5 HELIX 8 AA8 HIS B 78 ARG B 82 5 5 HELIX 9 AA9 LYS B 89 GLY B 95 5 7 HELIX 10 AB1 LYS B 105 ALA B 109 5 5 HELIX 11 AB2 PRO B 133 HIS B 140 1 8 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 5 LEU B 27 GLU B 31 0 SHEET 2 AA3 5 ALA B 121 ASN B 131 1 O LYS B 129 N TYR B 28 SHEET 3 AA3 5 GLY B 110 SER B 117 -1 N TYR B 112 O ILE B 126 SHEET 4 AA3 5 ILE B 54 MET B 59 -1 N TYR B 56 O MET B 115 SHEET 5 AA3 5 LYS B 62 VAL B 68 -1 O ILE B 64 N TRP B 57 SHEET 1 AA4 3 MET B 36 ILE B 38 0 SHEET 2 AA4 3 LEU B 99 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 SSBOND 1 CYS A 40 CYS A 114 1555 1555 1.98 SSBOND 2 CYS B 40 CYS B 114 1555 1555 2.04 CISPEP 1 LEU A 74 LYS A 75 0 9.55 SITE 1 AC1 19 PHE A 19 THR A 20 ILE A 54 TYR A 56 SITE 2 AC1 19 MET A 115 ALA A 121 ASP A 122 HOH A 229 SITE 3 AC1 19 ILE B 54 TYR B 56 GLN B 66 VAL B 68 SITE 4 AC1 19 MET B 115 ILE B 116 SER B 117 ALA B 121 SITE 5 AC1 19 ASP B 122 HOH B 306 HOH B 316 CRYST1 51.815 52.379 111.526 90.00 90.00 90.00 P 2 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 0.019299 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019092 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008967 0.00000