HEADER OXIDOREDUCTASE 06-SEP-17 5OX6 TITLE HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH VADADUSTAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: EGL NINE HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 181-426; COMPND 5 SYNONYM: HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2,HPH-2,PROLYL COMPND 6 HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2,PHD2,SM-20; COMPND 7 EC: 1.14.11.29; COMPND 8 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: EGLN1, C1ORF12, PNAS-118, PNAS-137; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS OXIDOREDUCTASE, NON-HEME DIOXYGENASE, IRON, 2-OXOGLUTARATE, HYPOXIA- KEYWDS 2 INDUCIBLE FACTOR, HIF, HIF PROLYL HYDROXYLASE DOMAIN 2, PHD2, EGLN1, KEYWDS 3 OXYGENASE, HYPOXIA, DNA-BINDING, METAL-BINDING, TRANSCRIPTION, KEYWDS 4 HELIX-LOOP-HELIX-BETA, DSBH, FACIAL TRIAD, CYTOPLASM, KEYWDS 5 TRANSCRIPTION/EPIGENETIC REGULATION, SIGNALING, DEVELOPMENT, CELL KEYWDS 6 STRUCTURE, BETA-HYDROXYLATION, TRANSCRIPTION ACTIVATOR/INHIBITOR, KEYWDS 7 UBL CONJUGATION, POLYMORPHISM, VITAMIN C, ZINC-FINGER, FAMILIAL KEYWDS 8 ERYTHROCYTOSIS, BREAST CANCER, TRANSCRIPTION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,D.ZHANG,C.J.SCHOFIELD REVDAT 3 17-JAN-24 5OX6 1 REMARK REVDAT 2 21-FEB-18 5OX6 1 JRNL REVDAT 1 18-OCT-17 5OX6 0 JRNL AUTH T.L.YEH,T.M.LEISSING,M.I.ABBOUD,C.C.THINNES,O.ATASOYLU, JRNL AUTH 2 J.P.HOLT-MARTYN,D.ZHANG,A.TUMBER,K.LIPPL,C.T.LOHANS, JRNL AUTH 3 I.K.H.LEUNG,H.MORCRETTE,I.J.CLIFTON,T.D.W.CLARIDGE, JRNL AUTH 4 A.KAWAMURA,E.FLASHMAN,X.LU,P.J.RATCLIFFE,R.CHOWDHURY, JRNL AUTH 5 C.W.PUGH,C.J.SCHOFIELD JRNL TITL MOLECULAR AND CELLULAR MECHANISMS OF HIF PROLYL HYDROXYLASE JRNL TITL 2 INHIBITORS IN CLINICAL TRIALS. JRNL REF CHEM SCI V. 8 7651 2017 JRNL REFN ISSN 2041-6520 JRNL PMID 29435217 JRNL DOI 10.1039/C7SC02103H REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.CHOWDHURY,J.I.CANDELA-LENA,M.C.CHAN,D.J.GREENALD,K.K.YEOH, REMARK 1 AUTH 2 Y.M.TIAN,M.A.MCDONOUGH,A.TUMBER,N.R.ROSE,A.CONEJO-GARCIA, REMARK 1 AUTH 3 M.DEMETRIADES,S.MATHAVAN,A.KAWAMURA,M.K.LEE,F.VAN EEDEN, REMARK 1 AUTH 4 C.W.PUGH,P.J.RATCLIFFE,C.J.SCHOFIELD REMARK 1 TITL SELECTIVE SMALL MOLECULE PROBES FOR THE HYPOXIA INDUCIBLE REMARK 1 TITL 2 FACTOR (HIF) PROLYL HYDROXYLASES. REMARK 1 REF ACS CHEM. BIOL. V. 8 1488 2013 REMARK 1 REFN ESSN 1554-8937 REMARK 1 PMID 23683440 REMARK 1 DOI 10.1021/CB400088Q REMARK 1 REFERENCE 2 REMARK 1 AUTH M.C.CHAN,O.ATASOYLU,E.HODSON,A.TUMBER,I.K.LEUNG,R.CHOWDHURY, REMARK 1 AUTH 2 V.GOMEZ-PEREZ,M.DEMETRIADES,A.M.RYDZIK,J.HOLT-MARTYN, REMARK 1 AUTH 3 Y.M.TIAN,T.BISHOP,T.D.CLARIDGE,A.KAWAMURA,C.W.PUGH, REMARK 1 AUTH 4 P.J.RATCLIFFE,C.J.SCHOFIELD REMARK 1 TITL POTENT AND SELECTIVE TRIAZOLE-BASED INHIBITORS OF THE REMARK 1 TITL 2 HYPOXIA-INDUCIBLE FACTOR PROLYL-HYDROXYLASES WITH ACTIVITY REMARK 1 TITL 3 IN THE MURINE BRAIN. REMARK 1 REF PLOS ONE V. 10 32004 2015 REMARK 1 REFN ESSN 1932-6203 REMARK 1 PMID 26147748 REMARK 1 DOI 10.1371/JOURNAL.PONE.0132004 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 19297 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.390 REMARK 3 FREE R VALUE TEST SET COUNT : 1040 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 36.3620 - 3.8057 0.99 2738 133 0.1637 0.1942 REMARK 3 2 3.8057 - 3.0211 0.99 2615 176 0.1508 0.1766 REMARK 3 3 3.0211 - 2.6394 0.99 2613 145 0.1599 0.2094 REMARK 3 4 2.6394 - 2.3981 0.98 2608 133 0.1888 0.1966 REMARK 3 5 2.3981 - 2.2262 0.98 2589 137 0.1993 0.2422 REMARK 3 6 2.2262 - 2.0950 0.97 2561 152 0.2305 0.2637 REMARK 3 7 2.0950 - 1.9901 0.97 2533 164 0.2719 0.3063 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 64.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.54000 REMARK 3 B22 (A**2) : -0.54000 REMARK 3 B33 (A**2) : 1.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.010 1851 REMARK 3 ANGLE : 1.027 2510 REMARK 3 CHIRALITY : 0.057 262 REMARK 3 PLANARITY : 0.007 329 REMARK 3 DIHEDRAL : 14.010 1080 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 188:204) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3072 127.8793 -0.5476 REMARK 3 T TENSOR REMARK 3 T11: 0.3173 T22: 0.3574 REMARK 3 T33: 0.6756 T12: -0.0456 REMARK 3 T13: -0.0439 T23: -0.0690 REMARK 3 L TENSOR REMARK 3 L11: 0.4489 L22: 0.5660 REMARK 3 L33: 0.9439 L12: -0.1374 REMARK 3 L13: -0.1168 L23: -0.6834 REMARK 3 S TENSOR REMARK 3 S11: 0.0511 S12: 0.0390 S13: 0.6041 REMARK 3 S21: -0.2169 S22: -0.1822 S23: -0.8704 REMARK 3 S31: 0.6745 S32: 0.2970 S33: -0.0313 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 205:215) REMARK 3 ORIGIN FOR THE GROUP (A): 31.2003 119.2103 -1.8161 REMARK 3 T TENSOR REMARK 3 T11: 0.0488 T22: 0.4173 REMARK 3 T33: 0.5646 T12: -0.0400 REMARK 3 T13: -0.1315 T23: -0.0614 REMARK 3 L TENSOR REMARK 3 L11: 1.1620 L22: 1.8416 REMARK 3 L33: 3.6119 L12: -0.8197 REMARK 3 L13: -0.0240 L23: 2.0702 REMARK 3 S TENSOR REMARK 3 S11: 0.5268 S12: -0.0309 S13: 0.3188 REMARK 3 S21: -0.2430 S22: 0.1720 S23: -1.2655 REMARK 3 S31: -0.7659 S32: 0.9960 S33: 0.4982 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 216:232) REMARK 3 ORIGIN FOR THE GROUP (A): 21.7371 105.9535 9.7172 REMARK 3 T TENSOR REMARK 3 T11: 0.6607 T22: 0.3466 REMARK 3 T33: 0.3723 T12: 0.0660 REMARK 3 T13: -0.2259 T23: 0.0690 REMARK 3 L TENSOR REMARK 3 L11: 2.4124 L22: 0.5908 REMARK 3 L33: 0.7515 L12: -0.6229 REMARK 3 L13: -0.2330 L23: 0.5831 REMARK 3 S TENSOR REMARK 3 S11: -0.1235 S12: 0.0192 S13: -0.8980 REMARK 3 S21: 1.2360 S22: 0.1049 S23: -0.3539 REMARK 3 S31: 0.8513 S32: 0.1764 S33: -0.1120 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 233:266) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8810 107.8290 -0.3183 REMARK 3 T TENSOR REMARK 3 T11: 0.4319 T22: 0.3455 REMARK 3 T33: 0.3877 T12: -0.0914 REMARK 3 T13: 0.0582 T23: -0.0855 REMARK 3 L TENSOR REMARK 3 L11: 1.2868 L22: 1.1611 REMARK 3 L33: 0.9568 L12: -0.7175 REMARK 3 L13: -0.8321 L23: -0.1666 REMARK 3 S TENSOR REMARK 3 S11: 0.0232 S12: 0.1685 S13: -0.4787 REMARK 3 S21: 0.6320 S22: -0.4358 S23: 0.7976 REMARK 3 S31: 0.6392 S32: -0.4506 S33: -0.1218 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 267:283) REMARK 3 ORIGIN FOR THE GROUP (A): 24.6904 123.3850 9.3189 REMARK 3 T TENSOR REMARK 3 T11: 0.5396 T22: 0.3713 REMARK 3 T33: 0.4055 T12: -0.0351 REMARK 3 T13: -0.1812 T23: -0.0808 REMARK 3 L TENSOR REMARK 3 L11: 1.1233 L22: 0.2619 REMARK 3 L33: 0.0516 L12: -0.5591 REMARK 3 L13: -0.3148 L23: 0.1267 REMARK 3 S TENSOR REMARK 3 S11: 0.0515 S12: -0.5698 S13: 0.5089 REMARK 3 S21: 0.9946 S22: 0.1758 S23: -0.4847 REMARK 3 S31: 0.2179 S32: 0.2239 S33: 0.0442 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 284:293) REMARK 3 ORIGIN FOR THE GROUP (A): 23.2164 135.7920 0.1011 REMARK 3 T TENSOR REMARK 3 T11: 0.3959 T22: 0.3482 REMARK 3 T33: 0.5899 T12: 0.0154 REMARK 3 T13: 0.0306 T23: -0.0262 REMARK 3 L TENSOR REMARK 3 L11: 0.2295 L22: 0.0429 REMARK 3 L33: 1.1882 L12: 0.0623 REMARK 3 L13: -0.5203 L23: -0.1161 REMARK 3 S TENSOR REMARK 3 S11: -0.0141 S12: 0.2552 S13: 0.9062 REMARK 3 S21: 0.0427 S22: 0.2092 S23: -0.7018 REMARK 3 S31: -0.4868 S32: -0.5373 S33: 0.0027 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 294:306) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3722 113.4744 0.6419 REMARK 3 T TENSOR REMARK 3 T11: 0.2881 T22: 0.2301 REMARK 3 T33: 0.2353 T12: -0.0221 REMARK 3 T13: -0.0031 T23: -0.0263 REMARK 3 L TENSOR REMARK 3 L11: 0.6569 L22: 0.4896 REMARK 3 L33: 0.9220 L12: -0.2652 REMARK 3 L13: 0.0661 L23: -0.6862 REMARK 3 S TENSOR REMARK 3 S11: 0.0378 S12: -0.0781 S13: -0.1698 REMARK 3 S21: 0.2204 S22: 0.2080 S23: -0.2160 REMARK 3 S31: 0.2423 S32: 0.2374 S33: -0.0005 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 307:320) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3781 119.8327 -10.6161 REMARK 3 T TENSOR REMARK 3 T11: 0.3603 T22: 0.3048 REMARK 3 T33: 0.3244 T12: 0.0327 REMARK 3 T13: -0.0763 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 0.7498 L22: 0.0308 REMARK 3 L33: 0.2840 L12: -0.1232 REMARK 3 L13: 0.4457 L23: -0.0488 REMARK 3 S TENSOR REMARK 3 S11: -0.0950 S12: 0.1782 S13: 0.2343 REMARK 3 S21: -0.3716 S22: -0.1636 S23: 0.5623 REMARK 3 S31: 0.0605 S32: -0.3494 S33: 0.0006 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 321:335) REMARK 3 ORIGIN FOR THE GROUP (A): 23.2980 113.8060 -1.6987 REMARK 3 T TENSOR REMARK 3 T11: 0.2050 T22: 0.2911 REMARK 3 T33: 0.3367 T12: 0.0176 REMARK 3 T13: -0.0537 T23: -0.0697 REMARK 3 L TENSOR REMARK 3 L11: 0.7651 L22: 1.8979 REMARK 3 L33: 0.6545 L12: 0.7820 REMARK 3 L13: 0.4458 L23: -0.0393 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: 0.2861 S13: -0.0994 REMARK 3 S21: 0.4115 S22: -0.0260 S23: -0.3895 REMARK 3 S31: -0.1627 S32: 0.3224 S33: -0.0349 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 336:350) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6588 114.4332 -14.7615 REMARK 3 T TENSOR REMARK 3 T11: 0.5179 T22: 0.3501 REMARK 3 T33: 0.3397 T12: 0.0599 REMARK 3 T13: 0.1302 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.8457 L22: 0.1945 REMARK 3 L33: 0.0970 L12: 0.1032 REMARK 3 L13: 0.2253 L23: 0.0730 REMARK 3 S TENSOR REMARK 3 S11: 0.1015 S12: 0.3876 S13: -0.0711 REMARK 3 S21: -0.8421 S22: 0.0469 S23: -0.2719 REMARK 3 S31: -0.0845 S32: 0.1598 S33: 0.0087 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 351:361) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1523 112.9387 -9.3339 REMARK 3 T TENSOR REMARK 3 T11: 0.3536 T22: 0.3929 REMARK 3 T33: 0.4396 T12: 0.0100 REMARK 3 T13: 0.0194 T23: -0.0385 REMARK 3 L TENSOR REMARK 3 L11: 0.3061 L22: 0.7583 REMARK 3 L33: 0.3926 L12: -0.3071 REMARK 3 L13: -0.1777 L23: 0.5621 REMARK 3 S TENSOR REMARK 3 S11: -0.1669 S12: 0.2511 S13: -0.2967 REMARK 3 S21: -0.0066 S22: -0.1135 S23: -1.0230 REMARK 3 S31: -0.1451 S32: 0.2988 S33: -0.0039 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 362:371) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4086 124.2440 -7.1520 REMARK 3 T TENSOR REMARK 3 T11: 0.3072 T22: 0.2580 REMARK 3 T33: 0.2885 T12: -0.0445 REMARK 3 T13: 0.0184 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.2010 L22: 0.7670 REMARK 3 L33: 0.3803 L12: 0.2171 REMARK 3 L13: -0.1138 L23: 0.3392 REMARK 3 S TENSOR REMARK 3 S11: 0.1772 S12: 0.1631 S13: 0.2123 REMARK 3 S21: -0.1724 S22: -0.1224 S23: -0.2967 REMARK 3 S31: -0.1092 S32: 0.0989 S33: -0.0001 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 372:381) REMARK 3 ORIGIN FOR THE GROUP (A): 18.6873 111.1358 -12.2898 REMARK 3 T TENSOR REMARK 3 T11: 0.4411 T22: 0.2755 REMARK 3 T33: 0.2195 T12: -0.0020 REMARK 3 T13: 0.0275 T23: -0.0499 REMARK 3 L TENSOR REMARK 3 L11: 0.2681 L22: 0.1634 REMARK 3 L33: 0.2185 L12: -0.2169 REMARK 3 L13: -0.2080 L23: 0.1872 REMARK 3 S TENSOR REMARK 3 S11: -0.0467 S12: 0.3109 S13: -0.1771 REMARK 3 S21: -0.8141 S22: 0.0087 S23: -0.9443 REMARK 3 S31: 0.2699 S32: -0.0406 S33: -0.0009 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 382:392) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8187 118.6248 0.3776 REMARK 3 T TENSOR REMARK 3 T11: 0.2920 T22: 0.2446 REMARK 3 T33: 0.2549 T12: -0.0226 REMARK 3 T13: -0.0448 T23: -0.0379 REMARK 3 L TENSOR REMARK 3 L11: 1.1490 L22: 0.1837 REMARK 3 L33: 0.3477 L12: 0.3206 REMARK 3 L13: -0.4204 L23: 0.0469 REMARK 3 S TENSOR REMARK 3 S11: 0.1060 S12: -0.0153 S13: 0.2272 REMARK 3 S21: 0.2534 S22: -0.1101 S23: -0.4671 REMARK 3 S31: 0.0663 S32: 0.1159 S33: -0.0003 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 393:403) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7398 135.9747 -1.7228 REMARK 3 T TENSOR REMARK 3 T11: 0.2971 T22: 0.2550 REMARK 3 T33: 0.4217 T12: 0.0489 REMARK 3 T13: -0.0194 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.0747 L22: 0.1276 REMARK 3 L33: 0.1873 L12: -0.1013 REMARK 3 L13: -0.1155 L23: 0.1532 REMARK 3 S TENSOR REMARK 3 S11: 0.0956 S12: 0.0620 S13: -0.5378 REMARK 3 S21: -0.6703 S22: 0.1403 S23: 0.1057 REMARK 3 S31: -0.4752 S32: 0.2482 S33: 0.0017 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 5OX6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97623 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19366 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 36.362 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.07600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 4BQX REMARK 200 REMARK 200 REMARK: HEXAGONAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6, 25% W/V POLYETHYLENE GLYCOL 4000, REMARK 280 SITTING DROP (300 NL), PROTEIN-TO-WELL RATIO, 2:1, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 19.98550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.98550 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.98550 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 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 GLY A 175 REMARK 465 SER A 176 REMARK 465 HIS A 177 REMARK 465 MET A 178 REMARK 465 ALA A 179 REMARK 465 SER A 180 REMARK 465 PRO A 181 REMARK 465 ASN A 182 REMARK 465 GLY A 183 REMARK 465 GLN A 184 REMARK 465 THR A 185 REMARK 465 LYS A 186 REMARK 465 PRO A 187 REMARK 465 THR A 405 REMARK 465 GLY A 406 REMARK 465 GLU A 407 REMARK 465 GLU A 413 REMARK 465 LEU A 414 REMARK 465 ASN A 415 REMARK 465 LYS A 416 REMARK 465 PRO A 417 REMARK 465 SER A 418 REMARK 465 ASP A 419 REMARK 465 SER A 420 REMARK 465 VAL A 421 REMARK 465 GLY A 422 REMARK 465 LYS A 423 REMARK 465 ASP A 424 REMARK 465 VAL A 425 REMARK 465 PHE A 426 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 216 CD CE NZ REMARK 470 SER A 242 OG REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 SER A 248 OG REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 GLU A 260 CD OE1 OE2 REMARK 470 LYS A 337 CG CD CE NZ REMARK 470 LYS A 400 CE NZ REMARK 470 LYS A 402 CG CD CE NZ REMARK 470 LEU A 404 CG CD1 CD2 REMARK 470 LYS A 408 CG CD CE NZ REMARK 470 ARG A 411 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 412 CG1 CG2 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 HH21 ARG A 396 O1 SO4 A 503 0.45 REMARK 500 O HOH A 705 O HOH A 717 1.94 REMARK 500 O HOH A 680 O HOH A 716 1.99 REMARK 500 O HOH A 613 O HOH A 668 2.00 REMARK 500 O HOH A 718 O HOH A 726 2.15 REMARK 500 O HOH A 641 O HOH A 695 2.17 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 A 197 -60.15 -132.03 REMARK 500 TYR A 197 -60.79 -132.03 REMARK 500 ALA A 351 39.83 -90.45 REMARK 500 TYR A 403 52.88 -117.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 313 NE2 REMARK 620 2 ASP A 315 OD1 95.8 REMARK 620 3 HIS A 374 NE2 90.0 92.9 REMARK 620 4 A1Z A 502 O10 95.1 168.6 90.6 REMARK 620 5 A1Z A 502 N11 89.2 101.5 165.6 75.2 REMARK 620 6 HOH A 616 O 177.0 87.2 90.4 82.0 89.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A1Z A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 DBREF 5OX6 A 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 SEQADV 5OX6 GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 5OX6 SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 5OX6 HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 5OX6 MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 5OX6 ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 5OX6 SER A 180 UNP Q9GZT9 EXPRESSION TAG SEQRES 1 A 252 GLY SER HIS MET ALA SER PRO ASN GLY GLN THR LYS PRO SEQRES 2 A 252 LEU PRO ALA LEU LYS LEU ALA LEU GLU TYR ILE VAL PRO SEQRES 3 A 252 CYS MET ASN LYS HIS GLY ILE CYS VAL VAL ASP ASP PHE SEQRES 4 A 252 LEU GLY LYS GLU THR GLY GLN GLN ILE GLY ASP GLU VAL SEQRES 5 A 252 ARG ALA LEU HIS ASP THR GLY LYS PHE THR ASP GLY GLN SEQRES 6 A 252 LEU VAL SER GLN LYS SER ASP SER SER LYS ASP ILE ARG SEQRES 7 A 252 GLY ASP LYS ILE THR TRP ILE GLU GLY LYS GLU PRO GLY SEQRES 8 A 252 CYS GLU THR ILE GLY LEU LEU MET SER SER MET ASP ASP SEQRES 9 A 252 LEU ILE ARG HIS CYS ASN GLY LYS LEU GLY SER TYR LYS SEQRES 10 A 252 ILE ASN GLY ARG THR LYS ALA MET VAL ALA CYS TYR PRO SEQRES 11 A 252 GLY ASN GLY THR GLY TYR VAL ARG HIS VAL ASP ASN PRO SEQRES 12 A 252 ASN GLY ASP GLY ARG CYS VAL THR CYS ILE TYR TYR LEU SEQRES 13 A 252 ASN LYS ASP TRP ASP ALA LYS VAL SER GLY GLY ILE LEU SEQRES 14 A 252 ARG ILE PHE PRO GLU GLY LYS ALA GLN PHE ALA ASP ILE SEQRES 15 A 252 GLU PRO LYS PHE ASP ARG LEU LEU PHE PHE TRP SER ASP SEQRES 16 A 252 ARG ARG ASN PRO HIS GLU VAL GLN PRO ALA TYR ALA THR SEQRES 17 A 252 ARG TYR ALA ILE THR VAL TRP TYR PHE ASP ALA ASP GLU SEQRES 18 A 252 ARG ALA ARG ALA LYS VAL LYS TYR LEU THR GLY GLU LYS SEQRES 19 A 252 GLY VAL ARG VAL GLU LEU ASN LYS PRO SER ASP SER VAL SEQRES 20 A 252 GLY LYS ASP VAL PHE HET MN A 501 1 HET A1Z A 502 31 HET SO4 A 503 5 HET SO4 A 504 5 HET GOL A 505 14 HET GOL A 506 13 HETNAM MN MANGANESE (II) ION HETNAM A1Z VADADUSTAT HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN A1Z GSK128863 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN MN 2+ FORMUL 3 A1Z C14 H11 CL N2 O4 FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *127(H2 O) HELIX 1 AA1 PRO A 189 TYR A 197 1 9 HELIX 2 AA2 TYR A 197 GLY A 206 1 10 HELIX 3 AA3 GLY A 215 THR A 232 1 18 HELIX 4 AA4 ASP A 246 ASP A 250 5 5 HELIX 5 AA5 CYS A 266 ASN A 284 1 19 HELIX 6 AA6 ASP A 335 GLY A 340 1 6 HELIX 7 AA7 ALA A 393 TYR A 403 1 11 SHEET 1 AA1 6 ILE A 207 VAL A 210 0 SHEET 2 AA1 6 ARG A 362 TRP A 367 -1 O LEU A 363 N VAL A 210 SHEET 3 AA1 6 ARG A 322 TYR A 329 -1 N THR A 325 O PHE A 366 SHEET 4 AA1 6 ARG A 383 ASP A 392 -1 O ILE A 386 N TYR A 328 SHEET 5 AA1 6 ALA A 298 TYR A 303 -1 N ALA A 301 O ALA A 385 SHEET 6 AA1 6 LYS A 255 ILE A 259 -1 N ILE A 259 O ALA A 298 SHEET 1 AA2 5 ILE A 207 VAL A 210 0 SHEET 2 AA2 5 ARG A 362 TRP A 367 -1 O LEU A 363 N VAL A 210 SHEET 3 AA2 5 ARG A 322 TYR A 329 -1 N THR A 325 O PHE A 366 SHEET 4 AA2 5 ARG A 383 ASP A 392 -1 O ILE A 386 N TYR A 328 SHEET 5 AA2 5 ILE A 292 ARG A 295 -1 N GLY A 294 O PHE A 391 SHEET 1 AA3 2 LEU A 240 SER A 242 0 SHEET 2 AA3 2 ILE A 251 ARG A 252 -1 O ILE A 251 N VAL A 241 SHEET 1 AA4 4 TYR A 310 HIS A 313 0 SHEET 2 AA4 4 HIS A 374 VAL A 376 -1 O HIS A 374 N HIS A 313 SHEET 3 AA4 4 LEU A 343 ILE A 345 -1 N ARG A 344 O GLU A 375 SHEET 4 AA4 4 ALA A 354 ILE A 356 -1 O ILE A 356 N LEU A 343 LINK NZ BLYS A 359 O3 SO4 A 504 1555 1555 1.30 LINK NH2 ARG A 396 O1 SO4 A 503 1555 1555 1.30 LINK NE2 HIS A 313 MN MN A 501 1555 1555 2.12 LINK OD1 ASP A 315 MN MN A 501 1555 1555 2.06 LINK NE2 HIS A 374 MN MN A 501 1555 1555 2.10 LINK MN MN A 501 O10 A1Z A 502 1555 1555 2.03 LINK MN MN A 501 N11 A1Z A 502 1555 1555 2.03 LINK MN MN A 501 O HOH A 616 1555 1555 2.12 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 A1Z A 502 SITE 2 AC1 5 HOH A 616 SITE 1 AC2 17 TRP A 258 MET A 299 TYR A 303 TYR A 310 SITE 2 AC2 17 HIS A 313 ASP A 315 TYR A 329 LEU A 343 SITE 3 AC2 17 HIS A 374 VAL A 376 ARG A 383 ARG A 398 SITE 4 AC2 17 VAL A 401 MN A 501 HOH A 605 HOH A 616 SITE 5 AC2 17 HOH A 652 SITE 1 AC3 2 ARG A 396 GLY A 409 SITE 1 AC4 3 GLU A 357 LYS A 359 ARG A 362 SITE 1 AC5 8 GLN A 243 SER A 247 ASP A 250 GLY A 288 SITE 2 AC5 8 SER A 289 TYR A 290 TRP A 367 ARG A 371 SITE 1 AC6 3 LYS A 262 ARG A 312 PRO A 373 CRYST1 111.088 111.088 39.971 90.00 90.00 120.00 P 63 6 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 0.009002 0.005197 0.000000 0.00000 SCALE2 0.000000 0.010394 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025018 0.00000