HEADER OXIDOREDUCTASE/TRANSCRIPTION 08-JUN-09 3HQR TITLE PHD2:MN:NOG:HIF1-ALPHA SUBSTRATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: EGL NINE HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD2 CATALYTIC DOMAIN, RESIDUES 181-426; COMPND 5 SYNONYM: PROLYL HYDROXYLASE, HYPOXIA-INDUCIBLE FACTOR PROLYL COMPND 6 HYDROXYLASE 2, HIF-PROLYL HYDROXYLASE 2, HIF-PH2, HPH-2, PROLYL COMPND 7 HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2, PHD2, SM-20; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA; COMPND 13 CHAIN: S; COMPND 14 FRAGMENT: C-TERMINAL DEGRADATION DOMAIN, RESIDUES 558-574; COMPND 15 SYNONYM: HIF-1 ALPHA, HIF1 ALPHA, ARNT-INTERACTING PROTEIN, MEMBER OF COMPND 16 PAS PROTEIN 1, BASIC-HELIX-LOOP-HELIX-PAS PROTEIN MOP1; 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: PHD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A(+); SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 OTHER_DETAILS: PEPTIDE SYNTHESIS KEYWDS DOUBLE STRANDED BETA-HELIX, ALTERNATIVE SPLICING, CONGENITAL KEYWDS 2 ERYTHROCYTOSIS, DIOXYGENASE, DISEASE MUTATION, IRON, METAL-BINDING, KEYWDS 3 OXIDOREDUCTASE, VITAMIN C, ZINC, ZINC-FINGER, ACTIVATOR, CYTOPLASM, KEYWDS 4 DNA-BINDING, HYDROXYLATION, ISOPEPTIDE BOND, NUCLEUS, KEYWDS 5 PHOSPHOPROTEIN, POLYMORPHISM, S-NITROSYLATION, TRANSCRIPTION, KEYWDS 6 TRANSCRIPTION REGULATION, UBL CONJUGATION, OXIDOREDUCTASE- KEYWDS 7 TRANSCRIPTION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,M.A.MCDONOUGH,C.J.SCHOFIELD REVDAT 4 01-NOV-23 3HQR 1 REMARK REVDAT 3 10-NOV-21 3HQR 1 REMARK SEQADV REVDAT 2 01-NOV-17 3HQR 1 REMARK REVDAT 1 28-JUL-09 3HQR 0 JRNL AUTH R.CHOWDHURY,M.A.MCDONOUGH,J.MECINOVIC,C.LOENARZ,E.FLASHMAN, JRNL AUTH 2 K.S.HEWITSON,C.DOMENE,C.J.SCHOFIELD JRNL TITL STRUCTURAL BASIS FOR BINDING OF HYPOXIA-INDUCIBLE FACTOR TO JRNL TITL 2 THE OXYGEN-SENSING PROLYL HYDROXYLASES JRNL REF STRUCTURE V. 17 981 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19604478 JRNL DOI 10.1016/J.STR.2009.06.002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.MCDONOUGH,V.LI,E.FLASHMAN,R.CHOWDHURY,C.MOHR, REMARK 1 AUTH 2 B.M.R.LIENARD,J.ZONDLO,N.J.OLDHAM,I.J.CLIFTON,J.LEWIS, REMARK 1 AUTH 3 L.A.MCNEILL,R.J.M.KURZEJA,K.S.HEWITSON,E.YANG,S.JORDAN, REMARK 1 AUTH 4 R.S.SYED,C.J.SCHOFIELD REMARK 1 TITL CELLULAR OXYGEN SENSING: CRYSTAL STRUCTURE OF REMARK 1 TITL 2 HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE (PHD2) REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 103 9814 2006 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 16782814 REMARK 1 DOI 10.1073/PNAS.0601283103 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 172620.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 13494 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 613 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2114 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 29 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.063 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1899 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.05000 REMARK 3 B22 (A**2) : 1.46000 REMARK 3 B33 (A**2) : 3.59000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 44.20 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : OGA.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : OGA.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HQR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053467. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : PT COATED MIRRORS IN A REMARK 200 KIRKPATRICK-BAEZ (KB) GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15231 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.15700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8790 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 REMARK 200 R SYM FOR SHELL (I) : 0.42000 REMARK 200 FOR SHELL : 1.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.2 REMARK 200 STARTING MODEL: PDB ENTRY 2G19 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 200MM MGCL2, PH 7.5, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.68950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.11050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.39900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.11050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.68950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.39900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, S 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 PRO A 181 REMARK 465 ASN A 182 REMARK 465 GLY A 183 REMARK 465 GLY A 409 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 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 196 CD OE1 OE2 REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 GLU A 267 CD OE1 OE2 REMARK 470 ASN A 284 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 GLY A 406 N - CA - C ANGL. DEV. = -18.9 DEGREES 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 -71.10 -136.42 REMARK 500 PHE A 235 152.07 -44.22 REMARK 500 SER A 245 150.31 65.60 REMARK 500 ASP A 246 -69.69 -22.50 REMARK 500 ASN A 284 -132.44 44.09 REMARK 500 PRO A 304 -21.72 -36.90 REMARK 500 ASP A 333 46.99 38.72 REMARK 500 PRO A 358 47.73 -77.77 REMARK 500 ASP A 369 -167.11 -71.00 REMARK 500 PRO A 378 124.05 -38.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 403 0.07 SIDE CHAIN 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 ASP A 315 OD1 REMARK 620 2 OGA A 600 O2 110.1 REMARK 620 3 OGA A 600 O2' 168.9 74.8 REMARK 620 4 HOH A1011 O 90.3 97.0 79.1 REMARK 620 N 1 2 3 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 OGA A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HQU RELATED DB: PDB REMARK 900 PHD2:FE:FG2:PARTIAL HIF1-ALPHA SUBSTRATE COMPLEX REMARK 900 RELATED ID: 2G1M RELATED DB: PDB REMARK 900 PHD2:INHIBITOR COMPLEX DBREF 3HQR A 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 DBREF 3HQR S 558 574 UNP Q16665 HIF1A_HUMAN 558 574 SEQADV 3HQR ALA A 398 UNP Q9GZT9 ARG 398 ENGINEERED MUTATION SEQRES 1 A 246 PRO ASN GLY GLN THR LYS PRO LEU PRO ALA LEU LYS LEU SEQRES 2 A 246 ALA LEU GLU TYR ILE VAL PRO CYS MET ASN LYS HIS GLY SEQRES 3 A 246 ILE CYS VAL VAL ASP ASP PHE LEU GLY LYS GLU THR GLY SEQRES 4 A 246 GLN GLN ILE GLY ASP GLU VAL ARG ALA LEU HIS ASP THR SEQRES 5 A 246 GLY LYS PHE THR ASP GLY GLN LEU VAL SER GLN LYS SER SEQRES 6 A 246 ASP SER SER LYS ASP ILE ARG GLY ASP LYS ILE THR TRP SEQRES 7 A 246 ILE GLU GLY LYS GLU PRO GLY CYS GLU THR ILE GLY LEU SEQRES 8 A 246 LEU MET SER SER MET ASP ASP LEU ILE ARG HIS CYS ASN SEQRES 9 A 246 GLY LYS LEU GLY SER TYR LYS ILE ASN GLY ARG THR LYS SEQRES 10 A 246 ALA MET VAL ALA CYS TYR PRO GLY ASN GLY THR GLY TYR SEQRES 11 A 246 VAL ARG HIS VAL ASP ASN PRO ASN GLY ASP GLY ARG CYS SEQRES 12 A 246 VAL THR CYS ILE TYR TYR LEU ASN LYS ASP TRP ASP ALA SEQRES 13 A 246 LYS VAL SER GLY GLY ILE LEU ARG ILE PHE PRO GLU GLY SEQRES 14 A 246 LYS ALA GLN PHE ALA ASP ILE GLU PRO LYS PHE ASP ARG SEQRES 15 A 246 LEU LEU PHE PHE TRP SER ASP ARG ARG ASN PRO HIS GLU SEQRES 16 A 246 VAL GLN PRO ALA TYR ALA THR ARG TYR ALA ILE THR VAL SEQRES 17 A 246 TRP TYR PHE ASP ALA ASP GLU ARG ALA ALA ALA LYS VAL SEQRES 18 A 246 LYS TYR LEU THR GLY GLU LYS GLY VAL ARG VAL GLU LEU SEQRES 19 A 246 ASN LYS PRO SER ASP SER VAL GLY LYS ASP VAL PHE SEQRES 1 S 17 ASP LEU GLU MET LEU ALA PRO TYR ILE PRO MET ASP ASP SEQRES 2 S 17 ASP PHE GLN LEU HET MN A 501 1 HET OGA A 600 10 HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE FORMUL 3 MN MN 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 HOH *151(H2 O) HELIX 1 1 PRO A 189 TYR A 197 1 9 HELIX 2 2 TYR A 197 GLY A 206 1 10 HELIX 3 3 LEU A 214 THR A 232 1 19 HELIX 4 4 SER A 247 ILE A 251 5 5 HELIX 5 5 CYS A 266 CYS A 283 1 18 HELIX 6 6 ASP A 335 GLY A 340 1 6 HELIX 7 7 ALA A 393 THR A 405 1 13 HELIX 8 8 ASP S 558 LEU S 562 5 5 SHEET 1 A 7 ILE A 207 VAL A 210 0 SHEET 2 A 7 LEU A 363 TRP A 367 -1 O PHE A 365 N CYS A 208 SHEET 3 A 7 ARG A 322 TYR A 329 -1 N ILE A 327 O LEU A 364 SHEET 4 A 7 ARG A 383 ASP A 392 -1 O TYR A 390 N VAL A 324 SHEET 5 A 7 ALA A 298 TYR A 303 -1 N MET A 299 O THR A 387 SHEET 6 A 7 LYS A 255 ILE A 259 -1 N THR A 257 O VAL A 300 SHEET 7 A 7 THR A 236 ASP A 237 -1 N THR A 236 O ILE A 256 SHEET 1 B 6 ILE A 207 VAL A 210 0 SHEET 2 B 6 LEU A 363 TRP A 367 -1 O PHE A 365 N CYS A 208 SHEET 3 B 6 ARG A 322 TYR A 329 -1 N ILE A 327 O LEU A 364 SHEET 4 B 6 ARG A 383 ASP A 392 -1 O TYR A 390 N VAL A 324 SHEET 5 B 6 ILE A 292 ARG A 295 -1 N GLY A 294 O PHE A 391 SHEET 6 B 6 PHE S 572 GLN S 573 -1 O PHE S 572 N ARG A 295 SHEET 1 C 4 THR A 308 HIS A 313 0 SHEET 2 C 4 HIS A 374 ALA A 379 -1 O ALA A 379 N THR A 308 SHEET 3 C 4 LEU A 343 ILE A 345 -1 N ARG A 344 O GLU A 375 SHEET 4 C 4 ALA A 354 ILE A 356 -1 O ILE A 356 N LEU A 343 SSBOND 1 CYS A 201 CYS A 208 1555 1555 2.03 LINK OD1 ASP A 315 MN MN A 501 1555 1555 1.96 LINK MN MN A 501 O2 OGA A 600 1555 1555 2.43 LINK MN MN A 501 O2' OGA A 600 1555 1555 2.01 LINK MN MN A 501 O HOH A1011 1555 1555 2.20 CISPEP 1 LYS A 186 PRO A 187 0 -1.27 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 OGA A 600 SITE 2 AC1 5 HOH A1011 SITE 1 AC2 16 MET A 299 TYR A 310 HIS A 313 ASP A 315 SITE 2 AC2 16 ILE A 327 TYR A 329 LEU A 343 HIS A 374 SITE 3 AC2 16 VAL A 376 ARG A 383 MN A 501 HOH A1005 SITE 4 AC2 16 HOH A1006 HOH A1011 HOH A1056 PRO S 564 CRYST1 39.379 68.798 72.221 90.00 90.00 90.00 P 21 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 0.025394 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013846 0.00000