HEADER IMMUNE SYSTEM 16-JAN-19 6NOJ TITLE PD-L1 IGV DOMAIN V76T WITH FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 18-134; COMPND 5 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 6 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 K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS FRAGMENT-BASED SCREENING, STRUCTURE-BASED DESIGN, PD-L1 INHIBITOR, KEYWDS 2 CANCER DRUG DISCOVERY, IMMUNOTHERAPY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHAO,E.PERRY REVDAT 5 16-OCT-24 6NOJ 1 REMARK REVDAT 4 11-OCT-23 6NOJ 1 REMARK REVDAT 3 27-NOV-19 6NOJ 1 REMARK REVDAT 2 06-MAR-19 6NOJ 1 JRNL REVDAT 1 20-FEB-19 6NOJ 0 JRNL AUTH E.PERRY,J.J.MILLS,B.ZHAO,F.WANG,Q.SUN,P.P.CHRISTOV,J.C.TARR, JRNL AUTH 2 T.A.RIETZ,E.T.OLEJNICZAK,T.LEE,S.FESIK JRNL TITL FRAGMENT-BASED SCREENING OF PROGRAMMED DEATH LIGAND 1 JRNL TITL 2 (PD-L1). JRNL REF BIOORG. MED. CHEM. LETT. V. 29 786 2019 JRNL REFN ESSN 1464-3405 JRNL PMID 30728114 JRNL DOI 10.1016/J.BMCL.2019.01.028 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 11900 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1190 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 27.0858 - 4.8387 1.00 1292 144 0.1680 0.2196 REMARK 3 2 4.8387 - 3.8441 1.00 1230 136 0.1477 0.1809 REMARK 3 3 3.8441 - 3.3592 1.00 1186 133 0.1730 0.2606 REMARK 3 4 3.3592 - 3.0526 1.00 1184 131 0.1941 0.2402 REMARK 3 5 3.0526 - 2.8340 0.99 1187 131 0.2250 0.2852 REMARK 3 6 2.8340 - 2.6671 0.99 1159 130 0.2168 0.2701 REMARK 3 7 2.6671 - 2.5336 1.00 1160 129 0.2292 0.2906 REMARK 3 8 2.5336 - 2.4234 0.99 1168 130 0.2433 0.3086 REMARK 3 9 2.4234 - 2.3302 0.99 1144 126 0.2575 0.3260 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.230 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 : 0.011 2030 REMARK 3 ANGLE : 1.259 2758 REMARK 3 CHIRALITY : 0.063 311 REMARK 3 PLANARITY : 0.008 351 REMARK 3 DIHEDRAL : 8.492 1199 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 19 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 69 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.8193 85.6853 24.3429 REMARK 3 T TENSOR REMARK 3 T11: 0.7108 T22: 0.8653 REMARK 3 T33: 0.6166 T12: -0.0773 REMARK 3 T13: 0.2541 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 0.7530 L22: 2.8338 REMARK 3 L33: 2.0030 L12: -1.4621 REMARK 3 L13: -0.3130 L23: 0.5739 REMARK 3 S TENSOR REMARK 3 S11: 1.1262 S12: -1.1274 S13: 0.2424 REMARK 3 S21: 0.6772 S22: -0.6670 S23: 0.4382 REMARK 3 S31: 1.6170 S32: 1.2227 S33: 0.3143 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 79 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3637 82.1412 25.8166 REMARK 3 T TENSOR REMARK 3 T11: 0.6553 T22: 0.5430 REMARK 3 T33: 0.1795 T12: -0.0298 REMARK 3 T13: 0.1667 T23: 0.0951 REMARK 3 L TENSOR REMARK 3 L11: 0.7231 L22: 4.0785 REMARK 3 L33: 1.4274 L12: 0.2818 REMARK 3 L13: -1.0089 L23: -0.5788 REMARK 3 S TENSOR REMARK 3 S11: 0.1129 S12: -0.8201 S13: 0.1510 REMARK 3 S21: 1.7985 S22: 0.2184 S23: 0.2877 REMARK 3 S31: 0.1025 S32: -0.0803 S33: 0.1664 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 85 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4455 75.4193 16.2969 REMARK 3 T TENSOR REMARK 3 T11: 0.3286 T22: 0.2883 REMARK 3 T33: 0.1999 T12: 0.0171 REMARK 3 T13: -0.0058 T23: 0.0334 REMARK 3 L TENSOR REMARK 3 L11: 7.9212 L22: 2.6129 REMARK 3 L33: 2.5928 L12: -1.3060 REMARK 3 L13: -2.4569 L23: -1.4146 REMARK 3 S TENSOR REMARK 3 S11: -0.3223 S12: -0.4031 S13: -0.3645 REMARK 3 S21: 0.4151 S22: 0.0031 S23: 0.0297 REMARK 3 S31: 0.3461 S32: 0.3859 S33: 0.4071 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 106 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3096 85.8787 12.4875 REMARK 3 T TENSOR REMARK 3 T11: 0.1884 T22: 0.1415 REMARK 3 T33: 0.1516 T12: -0.0376 REMARK 3 T13: -0.0124 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 2.2029 L22: 2.5884 REMARK 3 L33: 1.8089 L12: -0.0680 REMARK 3 L13: -1.5681 L23: -1.2689 REMARK 3 S TENSOR REMARK 3 S11: 0.3611 S12: -0.7437 S13: 0.2133 REMARK 3 S21: 0.2430 S22: -0.1927 S23: -0.2664 REMARK 3 S31: -0.1802 S32: 0.1623 S33: -0.0209 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 121 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0812 84.9667 7.7092 REMARK 3 T TENSOR REMARK 3 T11: 0.2127 T22: 0.2300 REMARK 3 T33: 0.2443 T12: 0.0673 REMARK 3 T13: 0.0013 T23: 0.0910 REMARK 3 L TENSOR REMARK 3 L11: 3.8215 L22: 4.1582 REMARK 3 L33: 1.6717 L12: 3.5550 REMARK 3 L13: -1.9996 L23: -1.1227 REMARK 3 S TENSOR REMARK 3 S11: 0.2591 S12: -0.3238 S13: 0.3157 REMARK 3 S21: 0.0206 S22: -0.2447 S23: -0.0742 REMARK 3 S31: -0.4500 S32: -0.2249 S33: -0.1574 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 132 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.9052 81.0852 20.9152 REMARK 3 T TENSOR REMARK 3 T11: 0.2032 T22: 0.3590 REMARK 3 T33: 0.3705 T12: -0.0219 REMARK 3 T13: 0.0037 T23: -0.0350 REMARK 3 L TENSOR REMARK 3 L11: 7.1326 L22: 3.4924 REMARK 3 L33: 3.6637 L12: 2.6180 REMARK 3 L13: 3.4694 L23: -0.9651 REMARK 3 S TENSOR REMARK 3 S11: 0.0738 S12: -0.9718 S13: 1.0071 REMARK 3 S21: 0.7183 S22: -0.5756 S23: 0.0482 REMARK 3 S31: -0.1706 S32: -1.0094 S33: -0.0803 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0426 103.9033 18.7309 REMARK 3 T TENSOR REMARK 3 T11: 0.3412 T22: 0.4263 REMARK 3 T33: 0.2679 T12: -0.0641 REMARK 3 T13: -0.0890 T23: -0.0620 REMARK 3 L TENSOR REMARK 3 L11: 7.7286 L22: 5.3551 REMARK 3 L33: 1.5033 L12: -1.4366 REMARK 3 L13: 0.8921 L23: -0.7797 REMARK 3 S TENSOR REMARK 3 S11: -0.2122 S12: -1.0099 S13: 0.6016 REMARK 3 S21: 0.7781 S22: 0.3784 S23: -0.2973 REMARK 3 S31: -0.4454 S32: 0.3727 S33: 0.2281 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.3441 109.9750 10.3378 REMARK 3 T TENSOR REMARK 3 T11: 0.2007 T22: 0.2413 REMARK 3 T33: 0.2306 T12: -0.0768 REMARK 3 T13: 0.0099 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 5.3987 L22: 2.7911 REMARK 3 L33: 1.3253 L12: -0.7768 REMARK 3 L13: 0.3432 L23: -0.4935 REMARK 3 S TENSOR REMARK 3 S11: 0.0681 S12: 0.0703 S13: 0.3717 REMARK 3 S21: 0.1871 S22: -0.2247 S23: -0.3591 REMARK 3 S31: 0.0605 S32: 0.1517 S33: 0.1359 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.8918 99.0809 4.3906 REMARK 3 T TENSOR REMARK 3 T11: 0.1350 T22: 0.2658 REMARK 3 T33: 0.2020 T12: 0.0219 REMARK 3 T13: 0.0543 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 5.2433 L22: 6.3526 REMARK 3 L33: 5.2773 L12: -1.9671 REMARK 3 L13: 3.1570 L23: 0.1714 REMARK 3 S TENSOR REMARK 3 S11: -0.0798 S12: 0.4698 S13: -0.5347 REMARK 3 S21: -0.1611 S22: -0.1006 S23: 0.0318 REMARK 3 S31: 0.5238 S32: 0.0388 S33: -0.1528 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.8079 99.3223 -3.1498 REMARK 3 T TENSOR REMARK 3 T11: 0.4430 T22: 0.6411 REMARK 3 T33: 0.2832 T12: 0.2201 REMARK 3 T13: -0.0326 T23: -0.0900 REMARK 3 L TENSOR REMARK 3 L11: 7.4874 L22: 7.0031 REMARK 3 L33: 3.8189 L12: -0.1732 REMARK 3 L13: 5.2121 L23: -1.2488 REMARK 3 S TENSOR REMARK 3 S11: -0.0245 S12: 0.4485 S13: -0.5953 REMARK 3 S21: -1.2467 S22: 0.0880 S23: -0.2253 REMARK 3 S31: 0.1912 S32: 0.9129 S33: -0.1014 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2248 106.5664 -4.4684 REMARK 3 T TENSOR REMARK 3 T11: 0.4317 T22: 0.4589 REMARK 3 T33: 0.4410 T12: 0.1630 REMARK 3 T13: -0.3212 T23: 0.0919 REMARK 3 L TENSOR REMARK 3 L11: 6.1557 L22: 2.0001 REMARK 3 L33: 2.0006 L12: 0.3410 REMARK 3 L13: 5.0129 L23: 3.1391 REMARK 3 S TENSOR REMARK 3 S11: 0.7784 S12: 1.6320 S13: -1.0999 REMARK 3 S21: -1.6795 S22: -0.4429 S23: 0.4335 REMARK 3 S31: 0.0445 S32: 0.8122 S33: 0.9268 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 85 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.9049 109.0495 4.9672 REMARK 3 T TENSOR REMARK 3 T11: 0.4309 T22: 0.4095 REMARK 3 T33: 0.4043 T12: -0.0047 REMARK 3 T13: 0.0012 T23: 0.0737 REMARK 3 L TENSOR REMARK 3 L11: 2.0048 L22: 3.0506 REMARK 3 L33: 3.4207 L12: 1.0974 REMARK 3 L13: 5.0180 L23: 2.4411 REMARK 3 S TENSOR REMARK 3 S11: -0.5156 S12: 1.6177 S13: 0.1500 REMARK 3 S21: -0.0006 S22: 0.2329 S23: -0.5120 REMARK 3 S31: -1.4718 S32: 0.5433 S33: 0.7055 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1828 105.6651 6.9740 REMARK 3 T TENSOR REMARK 3 T11: 0.1851 T22: 0.1887 REMARK 3 T33: 0.1545 T12: -0.0399 REMARK 3 T13: 0.0116 T23: 0.0515 REMARK 3 L TENSOR REMARK 3 L11: 6.3038 L22: 3.3443 REMARK 3 L33: 1.6002 L12: -2.5559 REMARK 3 L13: 0.3316 L23: -0.6797 REMARK 3 S TENSOR REMARK 3 S11: 0.0774 S12: 0.5593 S13: 0.2257 REMARK 3 S21: -0.4985 S22: -0.1444 S23: -0.4761 REMARK 3 S31: -0.0075 S32: 0.0210 S33: 0.1087 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1866 104.2956 13.7327 REMARK 3 T TENSOR REMARK 3 T11: 0.1787 T22: 0.1785 REMARK 3 T33: 0.2498 T12: -0.0119 REMARK 3 T13: 0.0399 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 4.3622 L22: 5.2811 REMARK 3 L33: 0.7875 L12: -4.8276 REMARK 3 L13: 1.7600 L23: -1.8905 REMARK 3 S TENSOR REMARK 3 S11: -0.3332 S12: -0.0663 S13: -0.0712 REMARK 3 S21: 0.6907 S22: 0.1791 S23: 0.1547 REMARK 3 S31: -0.1857 S32: 0.0849 S33: -0.0653 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2883 114.5925 0.2364 REMARK 3 T TENSOR REMARK 3 T11: 0.2148 T22: 0.4667 REMARK 3 T33: 0.3016 T12: -0.0309 REMARK 3 T13: -0.0341 T23: 0.0355 REMARK 3 L TENSOR REMARK 3 L11: 8.4625 L22: 7.9041 REMARK 3 L33: 5.6859 L12: -1.8087 REMARK 3 L13: -0.8207 L23: -0.9975 REMARK 3 S TENSOR REMARK 3 S11: -0.2415 S12: 1.8125 S13: 0.2912 REMARK 3 S21: -0.8553 S22: 0.4578 S23: 0.4690 REMARK 3 S31: 0.6525 S32: -0.1022 S33: -0.0988 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5868 82.4686 2.6034 REMARK 3 T TENSOR REMARK 3 T11: 0.2389 T22: 0.4717 REMARK 3 T33: 0.2777 T12: 0.0555 REMARK 3 T13: 0.0515 T23: 0.1000 REMARK 3 L TENSOR REMARK 3 L11: 2.5070 L22: 4.7110 REMARK 3 L33: 0.6104 L12: 2.0311 REMARK 3 L13: -0.1157 L23: 1.2473 REMARK 3 S TENSOR REMARK 3 S11: -0.4012 S12: 1.5730 S13: 0.0119 REMARK 3 S21: -0.7659 S22: 0.4575 S23: 0.1588 REMARK 3 S31: -0.1926 S32: 0.3406 S33: -0.0745 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 27 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0537 75.0317 13.0395 REMARK 3 T TENSOR REMARK 3 T11: 0.3016 T22: 0.1560 REMARK 3 T33: 0.2708 T12: 0.0568 REMARK 3 T13: -0.0462 T23: 0.0435 REMARK 3 L TENSOR REMARK 3 L11: 5.7352 L22: 0.8575 REMARK 3 L33: 1.4498 L12: 0.7078 REMARK 3 L13: -0.4213 L23: 0.2487 REMARK 3 S TENSOR REMARK 3 S11: 0.1192 S12: -0.1057 S13: -0.3236 REMARK 3 S21: -0.0716 S22: -0.2272 S23: 0.0634 REMARK 3 S31: 0.1745 S32: 0.0267 S33: 0.0016 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 39 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8293 78.5021 8.0625 REMARK 3 T TENSOR REMARK 3 T11: 0.3093 T22: 0.4838 REMARK 3 T33: 0.3244 T12: 0.1171 REMARK 3 T13: 0.1011 T23: 0.1604 REMARK 3 L TENSOR REMARK 3 L11: 2.4197 L22: 3.7924 REMARK 3 L33: 2.9233 L12: 1.3310 REMARK 3 L13: 2.3460 L23: 0.7950 REMARK 3 S TENSOR REMARK 3 S11: 0.2708 S12: -0.0872 S13: -0.7414 REMARK 3 S21: 0.0004 S22: -0.0047 S23: -0.6740 REMARK 3 S31: 0.0878 S32: 0.1428 S33: -0.1485 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 50 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9162 86.8297 17.2160 REMARK 3 T TENSOR REMARK 3 T11: 0.2027 T22: 0.2865 REMARK 3 T33: 0.2937 T12: -0.0110 REMARK 3 T13: 0.0543 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 7.9161 L22: 3.4210 REMARK 3 L33: 2.5859 L12: -1.0026 REMARK 3 L13: 0.3081 L23: 0.7283 REMARK 3 S TENSOR REMARK 3 S11: -0.2645 S12: -0.6803 S13: 1.5465 REMARK 3 S21: 0.3837 S22: 0.1280 S23: -0.0031 REMARK 3 S31: 0.1096 S32: 0.0185 S33: -0.0634 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 6NOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-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 : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16612 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : 0.09900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : 0.63500 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: PDB ENTRY 3BIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.056 M SODIUM PHOSPHATE MONOBASIC, REMARK 280 1.344 M POTASSIUM PHOSPHATE DIBASIC, EVAPORATION, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z 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 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 41.90150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.47050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.90150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.47050 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 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 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS B 144 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 41 NZ REMARK 470 GLU A 45 CB CG CD OE1 OE2 REMARK 470 LYS A 46 CB CG CD CE NZ REMARK 470 GLN A 47 CG CD OE1 NE2 REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 ASP A 90 CG OD1 OD2 REMARK 470 GLN A 91 CG CD OE1 NE2 REMARK 470 HIS A 139 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 45 CB CG CD OE1 OE2 REMARK 470 LYS B 46 CB CG CD CE NZ REMARK 470 ASP B 61 OD2 REMARK 470 LEU B 74 CG CD1 CD2 REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 LYS B 105 CG CD CE NZ REMARK 470 HIS B 139 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 143 CG ND1 CD2 CE1 NE2 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 GLU A 45 -76.78 -63.03 REMARK 500 LYS A 46 -103.70 -109.16 REMARK 500 GLU A 60 62.35 35.85 REMARK 500 ASP A 61 -0.19 76.92 REMARK 500 GLN A 83 -2.06 71.94 REMARK 500 ALA A 97 65.15 -101.18 REMARK 500 ASP A 103 77.90 41.62 REMARK 500 TYR A 118 83.90 -160.66 REMARK 500 GLU B 45 -74.94 -60.63 REMARK 500 LYS B 46 -102.64 -107.48 REMARK 500 GLU B 60 59.86 35.36 REMARK 500 ASP B 61 -2.55 79.75 REMARK 500 HIS B 69 66.51 33.46 REMARK 500 GLN B 83 -3.10 75.94 REMARK 500 ASP B 103 73.03 45.97 REMARK 500 TYR B 118 85.36 -159.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KW7 A 400 DBREF 6NOJ A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 DBREF 6NOJ B 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 SEQADV 6NOJ THR A 76 UNP Q9NZQ7 VAL 76 ENGINEERED MUTATION SEQADV 6NOJ ALA A 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ ALA A 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ ALA A 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ LEU A 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS A 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS A 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS A 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS A 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS A 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS A 144 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ THR B 76 UNP Q9NZQ7 VAL 76 ENGINEERED MUTATION SEQADV 6NOJ ALA B 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ ALA B 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ ALA B 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ LEU B 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS B 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS B 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS B 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS B 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS B 143 UNP Q9NZQ7 EXPRESSION TAG SEQADV 6NOJ HIS B 144 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 127 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 127 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 127 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 127 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 127 GLY GLU GLU ASP LEU LYS THR GLN HIS SER SER TYR ARG SEQRES 6 A 127 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 127 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 127 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 127 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 A 127 ALA ALA ALA LEU HIS HIS HIS HIS HIS HIS SEQRES 1 B 127 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 B 127 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 B 127 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 B 127 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 B 127 GLY GLU GLU ASP LEU LYS THR GLN HIS SER SER TYR ARG SEQRES 6 B 127 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 B 127 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 B 127 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 B 127 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 B 127 ALA ALA ALA LEU HIS HIS HIS HIS HIS HIS HET KW7 A 400 17 HETNAM KW7 METHYL 3-AMINO-4-(2-FLUOROPHENYL)-1H-PYRROLE-2- HETNAM 2 KW7 CARBOXYLATE FORMUL 3 KW7 C12 H11 F N2 O2 FORMUL 4 HOH *72(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 GLY A 95 5 7 HELIX 4 AA4 LYS A 105 ALA A 109 5 5 HELIX 5 AA5 PRO A 133 HIS A 142 1 10 HELIX 6 AA6 ASP B 49 ALA B 52 5 4 HELIX 7 AA7 HIS B 78 ARG B 82 5 5 HELIX 8 AA8 LEU B 88 SER B 93 1 6 HELIX 9 AA9 LYS B 105 ALA B 109 5 5 HELIX 10 AB1 PRO B 133 HIS B 142 1 10 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 ILE A 64 N TRP A 57 SHEET 6 AA1 6 GLU A 71 ASP A 73 -1 O ASP A 73 N GLN A 66 SHEET 1 AA2 3 MET A 36 ILE A 38 0 SHEET 2 AA2 3 LEU A 99 ILE A 101 -1 O LEU A 99 N ILE A 38 SHEET 3 AA2 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100 SHEET 1 AA3 6 LEU B 27 GLU B 31 0 SHEET 2 AA3 6 ALA B 121 ASN B 131 1 O LYS B 129 N VAL B 30 SHEET 3 AA3 6 GLY B 110 SER B 117 -1 N TYR B 112 O ILE B 126 SHEET 4 AA3 6 ILE B 54 MET B 59 -1 N TYR B 56 O MET B 115 SHEET 5 AA3 6 LYS B 62 VAL B 68 -1 O ILE B 64 N TRP B 57 SHEET 6 AA3 6 GLU B 71 ASP B 73 -1 O ASP B 73 N GLN B 66 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 2.03 SSBOND 2 CYS B 40 CYS B 114 1555 1555 2.09 SITE 1 AC1 11 TYR A 56 ILE A 116 SER A 117 ALA A 121 SITE 2 AC1 11 ASP A 122 ILE B 54 TYR B 56 MET B 115 SITE 3 AC1 11 ILE B 116 ALA B 121 ASP B 122 CRYST1 83.803 96.941 32.658 90.00 90.00 90.00 P 21 21 2 8 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 0.011933 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030620 0.00000