10 20 30 40 50 60 70 80 5L9B - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 10-JUN-16 5L9B
TITLE HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE TITLE 2 (2OG) AND HIF-1ALPHA CODD (556-574)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: EGL NINE HOMOLOG 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: 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; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HYPOXIA-INDUCIBLE FACTOR 1-ALPHA; COMPND 12 CHAIN: C, D; COMPND 13 FRAGMENT: UNP RESIDUES 556-574; COMPND 14 SYNONYM: HIF1-ALPHA,ARNT-INTERACTING PROTEIN,BASIC-HELIX-LOOP-HELIX- COMPND 15 PAS PROTEIN MOP1,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 78,BHLHE78, COMPND 16 MEMBER OF PAS PROTEIN 1,PAS DOMAIN-CONTAINING PROTEIN 8; COMPND 17 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(+); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606
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,C.J.SCHOFIELD
REVDAT 2 07-SEP-16 5L9B 1 JRNL REVDAT 1 31-AUG-16 5L9B 0
JRNL AUTH R.CHOWDHURY,I.K.LEUNG,Y.M.TIAN,M.I.ABBOUD,W.GE,C.DOMENE, JRNL AUTH 2 F.X.CANTRELLE,I.LANDRIEU,A.P.HARDY,C.W.PUGH,P.J.RATCLIFFE, JRNL AUTH 3 T.D.CLARIDGE,C.J.SCHOFIELD JRNL TITL STRUCTURAL BASIS FOR OXYGEN DEGRADATION DOMAIN SELECTIVITY JRNL TITL 2 OF THE HIF PROLYL HYDROXYLASES. JRNL REF NAT COMMUN V. 7 12673 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27561929 JRNL DOI 10.1038/NCOMMS12673
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.CHOWDHURY,M.A.MCDONOUGH,J.MECINOVIC,C.LOENARZ,E.FLASHMAN, REMARK 1 AUTH 2 K.S.HEWITSON,C.DOMENE,C.J.SCHOFIELD REMARK 1 TITL STRUCTURAL BASIS FOR BINDING OF HYPOXIA-INDUCIBLE FACTOR TO REMARK 1 TITL 2 THE OXYGEN-SENSING PROLYL HYDROXYLASES. REMARK 1 REF STRUCTURE V. 17 981 2009 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 19604478 REMARK 1 DOI 10.1016/J.STR.2009.06.002 REMARK 1 REFERENCE 2 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 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 31079 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1609 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 12.8992 - 4.2919 0.93 2694 179 0.1447 0.1519 REMARK 3 2 4.2919 - 3.4276 0.94 2686 168 0.1203 0.1586 REMARK 3 3 3.4276 - 3.0006 0.96 2709 113 0.1305 0.1777 REMARK 3 4 3.0006 - 2.7291 0.92 2601 195 0.1449 0.1646 REMARK 3 5 2.7291 - 2.5351 0.93 2628 176 0.1663 0.2102 REMARK 3 6 2.5351 - 2.3866 0.95 2681 136 0.1649 0.2253 REMARK 3 7 2.3866 - 2.2677 0.95 2679 116 0.1785 0.2288 REMARK 3 8 2.2677 - 2.1695 0.94 2667 134 0.1911 0.2367 REMARK 3 9 2.1695 - 2.0863 0.94 2638 126 0.2020 0.2369 REMARK 3 10 2.0863 - 2.0146 0.94 2644 116 0.2199 0.2519 REMARK 3 11 2.0146 - 1.9519 0.93 2645 142 0.2327 0.2649 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 : 0.40 REMARK 3 B_SOL : 60.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.26840 REMARK 3 B22 (A**2) : -6.15450 REMARK 3 B33 (A**2) : -0.11390 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.75570 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.4380 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 3769 REMARK 3 ANGLE : 0.610 5111 REMARK 3 CHIRALITY : 0.045 550 REMARK 3 PLANARITY : 0.004 672 REMARK 3 DIHEDRAL : 12.850 2221 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5L9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000373.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31425 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 40.193 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.6543 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.713 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: 3HQR REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M BIS-TRIS PH 5.5, 25% W/V POLYETHYLENE GLYCOL 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 38.19750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 VAL A 410 REMARK 465 ARG A 411 REMARK 465 VAL A 412 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 465 GLY B 175 REMARK 465 SER B 176 REMARK 465 HIS B 177 REMARK 465 MET B 178 REMARK 465 ALA B 179 REMARK 465 SER B 180 REMARK 465 PRO B 181 REMARK 465 ASN B 182 REMARK 465 GLY B 183 REMARK 465 GLN B 184 REMARK 465 THR B 185 REMARK 465 LYS B 186 REMARK 465 PRO B 187 REMARK 465 GLY B 406 REMARK 465 GLU B 407 REMARK 465 LYS B 408 REMARK 465 GLY B 409 REMARK 465 VAL B 410 REMARK 465 ARG B 411 REMARK 465 VAL B 412 REMARK 465 GLU B 413 REMARK 465 LEU B 414 REMARK 465 ASN B 415 REMARK 465 LYS B 416 REMARK 465 PRO B 417 REMARK 465 SER B 418 REMARK 465 ASP B 419 REMARK 465 SER B 420 REMARK 465 VAL B 421 REMARK 465 GLY B 422 REMARK 465 LYS B 423 REMARK 465 ASP B 424 REMARK 465 VAL B 425 REMARK 465 PHE B 426 REMARK 465 ASP C 556 REMARK 465 ASP D 556
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 192 CD CE NZ REMARK 470 GLU A 196 CG CD OE1 OE2 REMARK 470 LYS A 204 CD CE NZ REMARK 470 LYS A 216 CD CE NZ REMARK 470 LYS A 234 CG CD CE NZ REMARK 470 GLU A 260 OE1 OE2 REMARK 470 LYS A 262 CD CE NZ REMARK 470 GLU A 267 CD OE1 OE2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 337 CD CE NZ REMARK 470 LYS A 350 CG CD CE NZ REMARK 470 LYS A 402 CG CD CE NZ REMARK 470 GLU A 407 CG CD OE1 OE2 REMARK 470 LYS A 408 CD CE NZ REMARK 470 LYS B 192 CD CE NZ REMARK 470 GLU B 196 CD OE1 OE2 REMARK 470 LYS B 216 CD CE NZ REMARK 470 GLU B 217 OE1 OE2 REMARK 470 LYS B 234 CG CD CE NZ REMARK 470 GLU B 260 CD OE1 OE2 REMARK 470 LYS B 262 CD CE NZ REMARK 470 GLU B 267 CD OE1 OE2 REMARK 470 ASN B 284 CG OD1 ND2 REMARK 470 LYS B 286 CD CE NZ REMARK 470 LYS B 291 CG CD CE NZ REMARK 470 LYS B 402 NZ REMARK 470 GLU C 560 CG CD OE1 OE2 REMARK 470 GLU D 560 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 LYS B 402 O HOH B 601 2.08 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 -57.90 -140.70 REMARK 500 ILE A 251 -62.10 -102.46 REMARK 500 ASN A 284 -142.50 55.40 REMARK 500 ASN A 306 39.67 -96.58 REMARK 500 LEU A 330 15.35 -140.09 REMARK 500 ASP A 369 -166.25 -74.84 REMARK 500 THR A 405 -74.70 -121.29 REMARK 500 GLU A 407 -138.21 55.35 REMARK 500 TYR B 197 -58.25 -134.13 REMARK 500 ASN B 284 -133.52 50.92 REMARK 500 PRO B 304 48.77 -75.17 REMARK 500 PHE B 346 69.99 -112.40 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 747 DISTANCE = 5.87 ANGSTROMS
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 98.0 REMARK 620 3 HIS A 374 NE2 91.6 95.9 REMARK 620 4 HOH A 647 O 170.7 91.1 85.4 REMARK 620 5 AKG A 502 O1 93.6 101.8 160.6 86.5 REMARK 620 6 AKG A 502 O5 95.5 166.3 85.9 75.5 75.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 313 NE2 REMARK 620 2 ASP B 315 OD1 81.4 REMARK 620 3 HIS B 374 NE2 92.4 91.8 REMARK 620 4 AKG B 502 O2 88.3 102.2 165.9 REMARK 620 5 AKG B 502 O5 95.8 177.1 88.8 77.1 REMARK 620 6 HOH B 618 O 173.9 92.7 89.2 91.6 90.1 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 AKG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 502
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HQR RELATED DB: PDB REMARK 900 RELATED ID: 4BQY RELATED DB: PDB REMARK 900 RELATED ID: 5L9R RELATED DB: PDB
DBREF 5L9B A 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 DBREF 5L9B B 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 DBREF 5L9B C 556 574 UNP Q16665 HIF1A_HUMAN 556 574 DBREF 5L9B D 556 574 UNP Q16665 HIF1A_HUMAN 556 574
SEQADV 5L9B GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B SER A 180 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B ALA A 201 UNP Q9GZT9 CYS 201 ENGINEERED MUTATION SEQADV 5L9B ALA A 398 UNP Q9GZT9 ARG 398 ENGINEERED MUTATION SEQADV 5L9B GLY B 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B SER B 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B HIS B 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B MET B 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B ALA B 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B SER B 180 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9B ALA B 201 UNP Q9GZT9 CYS 201 ENGINEERED MUTATION SEQADV 5L9B ALA B 398 UNP Q9GZT9 ARG 398 ENGINEERED MUTATION
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 ALA 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 ALA 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 SEQRES 1 B 252 GLY SER HIS MET ALA SER PRO ASN GLY GLN THR LYS PRO SEQRES 2 B 252 LEU PRO ALA LEU LYS LEU ALA LEU GLU TYR ILE VAL PRO SEQRES 3 B 252 ALA MET ASN LYS HIS GLY ILE CYS VAL VAL ASP ASP PHE SEQRES 4 B 252 LEU GLY LYS GLU THR GLY GLN GLN ILE GLY ASP GLU VAL SEQRES 5 B 252 ARG ALA LEU HIS ASP THR GLY LYS PHE THR ASP GLY GLN SEQRES 6 B 252 LEU VAL SER GLN LYS SER ASP SER SER LYS ASP ILE ARG SEQRES 7 B 252 GLY ASP LYS ILE THR TRP ILE GLU GLY LYS GLU PRO GLY SEQRES 8 B 252 CYS GLU THR ILE GLY LEU LEU MET SER SER MET ASP ASP SEQRES 9 B 252 LEU ILE ARG HIS CYS ASN GLY LYS LEU GLY SER TYR LYS SEQRES 10 B 252 ILE ASN GLY ARG THR LYS ALA MET VAL ALA CYS TYR PRO SEQRES 11 B 252 GLY ASN GLY THR GLY TYR VAL ARG HIS VAL ASP ASN PRO SEQRES 12 B 252 ASN GLY ASP GLY ARG CYS VAL THR CYS ILE TYR TYR LEU SEQRES 13 B 252 ASN LYS ASP TRP ASP ALA LYS VAL SER GLY GLY ILE LEU SEQRES 14 B 252 ARG ILE PHE PRO GLU GLY LYS ALA GLN PHE ALA ASP ILE SEQRES 15 B 252 GLU PRO LYS PHE ASP ARG LEU LEU PHE PHE TRP SER ASP SEQRES 16 B 252 ARG ARG ASN PRO HIS GLU VAL GLN PRO ALA TYR ALA THR SEQRES 17 B 252 ARG TYR ALA ILE THR VAL TRP TYR PHE ASP ALA ASP GLU SEQRES 18 B 252 ARG ALA ALA ALA LYS VAL LYS TYR LEU THR GLY GLU LYS SEQRES 19 B 252 GLY VAL ARG VAL GLU LEU ASN LYS PRO SER ASP SER VAL SEQRES 20 B 252 GLY LYS ASP VAL PHE SEQRES 1 C 19 ASP LEU ASP LEU GLU MET LEU ALA PRO TYR ILE PRO MET SEQRES 2 C 19 ASP ASP ASP PHE GLN LEU SEQRES 1 D 19 ASP LEU ASP LEU GLU MET LEU ALA PRO TYR ILE PRO MET SEQRES 2 D 19 ASP ASP ASP PHE GLN LEU
HET MN A 501 1 HET AKG A 502 10 HET MN B 501 1 HET AKG B 502 10
HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID
FORMUL 5 MN 2(MN 2+) FORMUL 6 AKG 2(C5 H6 O5) FORMUL 9 HOH *298(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 SER A 247 ILE A 251 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 THR A 405 1 13 HELIX 8 AA8 PRO B 189 TYR B 197 1 9 HELIX 9 AA9 TYR B 197 GLY B 206 1 10 HELIX 10 AB1 GLY B 215 THR B 232 1 18 HELIX 11 AB2 SER B 247 ILE B 251 5 5 HELIX 12 AB3 CYS B 266 CYS B 283 1 18 HELIX 13 AB4 ASP B 335 GLY B 340 1 6 HELIX 14 AB5 ALA B 393 THR B 405 1 13 HELIX 15 AB6 ASP C 558 ALA C 563 5 6 HELIX 16 AB7 ASP D 558 LEU D 562 5 5
SHEET 1 AA1 7 ILE A 207 VAL A 210 0 SHEET 2 AA1 7 LEU A 363 TRP A 367 -1 O LEU A 363 N VAL A 210 SHEET 3 AA1 7 ARG A 322 TYR A 329 -1 N THR A 325 O PHE A 366 SHEET 4 AA1 7 ARG A 383 ASP A 392 -1 O ILE A 386 N TYR A 328 SHEET 5 AA1 7 ALA A 298 TYR A 303 -1 N MET A 299 O THR A 387 SHEET 6 AA1 7 LYS A 255 ILE A 259 -1 N LYS A 255 O CYS A 302 SHEET 7 AA1 7 THR A 236 ASP A 237 -1 N THR A 236 O ILE A 256 SHEET 1 AA2 6 ILE A 207 VAL A 210 0 SHEET 2 AA2 6 LEU A 363 TRP A 367 -1 O LEU A 363 N VAL A 210 SHEET 3 AA2 6 ARG A 322 TYR A 329 -1 N THR A 325 O PHE A 366 SHEET 4 AA2 6 ARG A 383 ASP A 392 -1 O ILE A 386 N TYR A 328 SHEET 5 AA2 6 ILE A 292 ARG A 295 -1 N GLY A 294 O PHE A 391 SHEET 6 AA2 6 PHE C 572 GLN C 573 -1 O PHE C 572 N ARG A 295 SHEET 1 AA3 4 THR A 308 HIS A 313 0 SHEET 2 AA3 4 HIS A 374 ALA A 379 -1 O HIS A 374 N HIS A 313 SHEET 3 AA3 4 LEU A 343 ILE A 345 -1 N ARG A 344 O GLU A 375 SHEET 4 AA3 4 ALA A 354 ILE A 356 -1 O ILE A 356 N LEU A 343 SHEET 1 AA4 7 ILE B 207 VAL B 210 0 SHEET 2 AA4 7 LEU B 363 TRP B 367 -1 O LEU B 363 N VAL B 210 SHEET 3 AA4 7 ARG B 322 TYR B 329 -1 N THR B 325 O PHE B 366 SHEET 4 AA4 7 THR B 382 ASP B 392 -1 O ILE B 386 N TYR B 328 SHEET 5 AA4 7 ALA B 298 PRO B 304 -1 N ALA B 301 O ALA B 385 SHEET 6 AA4 7 LYS B 255 ILE B 259 -1 N THR B 257 O VAL B 300 SHEET 7 AA4 7 THR B 236 ASP B 237 -1 N THR B 236 O ILE B 256 SHEET 1 AA5 6 ILE B 207 VAL B 210 0 SHEET 2 AA5 6 LEU B 363 TRP B 367 -1 O LEU B 363 N VAL B 210 SHEET 3 AA5 6 ARG B 322 TYR B 329 -1 N THR B 325 O PHE B 366 SHEET 4 AA5 6 THR B 382 ASP B 392 -1 O ILE B 386 N TYR B 328 SHEET 5 AA5 6 ILE B 292 ARG B 295 -1 N GLY B 294 O PHE B 391 SHEET 6 AA5 6 PHE D 572 GLN D 573 -1 O PHE D 572 N ARG B 295 SHEET 1 AA6 4 TYR B 310 HIS B 313 0 SHEET 2 AA6 4 HIS B 374 VAL B 376 -1 O VAL B 376 N TYR B 310 SHEET 3 AA6 4 LEU B 343 ILE B 345 -1 N ARG B 344 O GLU B 375 SHEET 4 AA6 4 ALA B 354 ILE B 356 -1 O ALA B 354 N ILE B 345
LINK NE2 HIS A 313 MN MN A 501 1555 1555 2.17 LINK OD1 ASP A 315 MN MN A 501 1555 1555 2.19 LINK NE2 HIS A 374 MN MN A 501 1555 1555 2.10 LINK NE2 HIS B 313 MN MN B 501 1555 1555 2.29 LINK OD1 ASP B 315 MN MN B 501 1555 1555 2.11 LINK NE2 HIS B 374 MN MN B 501 1555 1555 2.06 LINK MN MN A 501 O HOH A 647 1555 1555 2.28 LINK MN MN A 501 O1 AKG A 502 1555 1555 2.32 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.25 LINK MN MN B 501 O2 AKG B 502 1555 1555 2.21 LINK MN MN B 501 O5 AKG B 502 1555 1555 2.29 LINK MN MN B 501 O HOH B 618 1555 1555 2.38
SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 AKG A 502 SITE 2 AC1 5 HOH A 647 SITE 1 AC2 15 ARG A 252 MET A 299 TYR A 310 HIS A 313 SITE 2 AC2 15 ASP A 315 ILE A 327 TYR A 329 HIS A 374 SITE 3 AC2 15 VAL A 376 ARG A 383 MN A 501 HOH A 607 SITE 4 AC2 15 HOH A 613 HOH A 647 PRO C 564 SITE 1 AC3 5 HIS B 313 ASP B 315 HIS B 374 AKG B 502 SITE 2 AC3 5 HOH B 618 SITE 1 AC4 13 MET B 299 TYR B 310 HIS B 313 ASP B 315 SITE 2 AC4 13 TYR B 329 HIS B 374 VAL B 376 ARG B 383 SITE 3 AC4 13 MN B 501 HOH B 639 HOH B 648 HOH B 660 SITE 4 AC4 13 PRO D 564
CRYST1 40.193 76.395 70.962 90.00 90.03 90.00 P 1 21 1 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 0.024880 0.000000 0.000015 0.00000
SCALE2 0.000000 0.013090 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014092 0.00000