HEADER OXIDOREDUCTASE 11-JUN-16 5L9V TITLE HIF PROLYL HYDROXYLASE 2 (PHD2-R281C/P317C) CROSS-LINKED TO HIF-1ALPHA TITLE 2 NODD-L397C/D412C AND N-OXALYLGLYCINE (NOG) (COMPLEX-1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: EGL NINE HOMOLOG 1; COMPND 3 CHAIN: A, B; 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; 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: N-TERMINAL OXYGEN DEPENDENT DEGRADATION DOMAIN (NODD), UNP COMPND 14 RESIDUES 395-413; COMPND 15 SYNONYM: HIF1-ALPHA,ARNT-INTERACTING PROTEIN,BASIC-HELIX-LOOP-HELIX- COMPND 16 PAS PROTEIN MOP1,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 78,BHLHE78, COMPND 17 MEMBER OF PAS PROTEIN 1,PAS DOMAIN-CONTAINING PROTEIN 8; COMPND 18 ENGINEERED: YES; COMPND 19 MUTATION: 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; 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: SYNTHETIC PEPTIDE 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 4 10-JAN-24 5L9V 1 LINK REVDAT 3 29-NOV-17 5L9V 1 REMARK REVDAT 2 07-SEP-16 5L9V 1 JRNL REVDAT 1 31-AUG-16 5L9V 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 2 REMARK 2 RESOLUTION. 1.83 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 38938 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1960 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 43.8104 - 4.4078 0.99 2676 152 0.1484 0.1623 REMARK 3 2 4.4078 - 3.4991 0.99 2678 127 0.1390 0.1615 REMARK 3 3 3.4991 - 3.0569 0.99 2635 142 0.1621 0.1718 REMARK 3 4 3.0569 - 2.7774 1.00 2692 128 0.1577 0.1892 REMARK 3 5 2.7774 - 2.5784 1.00 2602 168 0.1741 0.1887 REMARK 3 6 2.5784 - 2.4264 1.00 2613 169 0.1724 0.1962 REMARK 3 7 2.4264 - 2.3049 1.00 2670 135 0.1766 0.1946 REMARK 3 8 2.3049 - 2.2045 1.00 2669 121 0.1773 0.2179 REMARK 3 9 2.2045 - 2.1197 1.00 2650 162 0.1829 0.2216 REMARK 3 10 2.1197 - 2.0465 1.00 2678 125 0.1965 0.2273 REMARK 3 11 2.0465 - 1.9825 1.00 2616 138 0.2139 0.2614 REMARK 3 12 1.9825 - 1.9259 1.00 2674 127 0.2481 0.2354 REMARK 3 13 1.9259 - 1.8752 1.00 2670 136 0.2669 0.2670 REMARK 3 14 1.8752 - 1.8294 0.93 2455 130 0.2869 0.3194 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 : 0.40 REMARK 3 B_SOL : 60.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.31000 REMARK 3 B22 (A**2) : 18.62000 REMARK 3 B33 (A**2) : -10.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 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 : 0.005 3726 REMARK 3 ANGLE : 0.711 5059 REMARK 3 CHIRALITY : 0.047 545 REMARK 3 PLANARITY : 0.003 664 REMARK 3 DIHEDRAL : 13.877 2219 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 5L9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000392. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-11 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 : DIAMOND REMARK 200 BEAMLINE : I04 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38965 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.829 REMARK 200 RESOLUTION RANGE LOW (A) : 43.798 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3375 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.90800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 20 % W/V REMARK 280 POLYETHYLENE GLYCOL 3350, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 36.54400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 LEU A 188 REMARK 465 LEU A 404 REMARK 465 THR A 405 REMARK 465 GLY A 406 REMARK 465 GLU A 407 REMARK 465 LYS A 408 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 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 LEU B 188 REMARK 465 LEU B 404 REMARK 465 THR B 405 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 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 CG CD CE NZ REMARK 470 GLU A 196 CD OE1 OE2 REMARK 470 LYS A 216 CE NZ REMARK 470 GLU A 217 CG CD OE1 OE2 REMARK 470 LYS A 262 CE NZ REMARK 470 LYS A 291 CD CE NZ REMARK 470 GLU A 348 CG CD OE1 OE2 REMARK 470 LYS A 350 CG CD CE NZ REMARK 470 LEU B 191 CG CD1 CD2 REMARK 470 LYS B 192 CG CD CE NZ REMARK 470 GLU B 196 CD OE1 OE2 REMARK 470 LYS B 216 CG CD CE NZ REMARK 470 GLU B 217 CG CD OE1 OE2 REMARK 470 SER B 245 OG REMARK 470 ASP B 246 CG OD1 OD2 REMARK 470 GLU B 260 CD OE1 OE2 REMARK 470 LYS B 262 CG CD CE NZ REMARK 470 LYS B 286 CG CD CE NZ REMARK 470 LYS B 291 CG CD CE NZ REMARK 470 GLU B 348 CG CD OE1 OE2 REMARK 470 VAL B 401 CG1 CG2 REMARK 470 LYS B 402 CG CD CE NZ 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 370 O HOH A 601 1.52 REMARK 500 O ASP B 278 HD1 HIS B 282 1.55 REMARK 500 O HOH C 510 O HOH C 512 2.03 REMARK 500 O HOH B 663 O HOH B 676 2.03 REMARK 500 O HOH A 693 O HOH C 513 2.04 REMARK 500 O HOH A 647 O HOH A 683 2.10 REMARK 500 O HOH A 685 O HOH A 702 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 692 O HOH A 702 1455 2.07 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 PHE A 346 75.82 -118.00 REMARK 500 ALA A 351 0.56 -65.98 REMARK 500 TYR B 197 -57.67 -138.46 REMARK 500 ILE B 251 -60.21 -91.61 REMARK 500 PHE B 346 79.36 -118.21 REMARK 500 CYS C 412 -52.13 71.75 REMARK 500 CYS D 412 -50.54 71.22 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 92.3 REMARK 620 3 HIS A 374 NE2 89.1 93.9 REMARK 620 4 OGA A 502 O2 93.9 100.5 165.2 REMARK 620 5 OGA A 502 O2' 96.1 171.0 83.0 82.2 REMARK 620 6 HOH A 626 O 176.4 91.2 90.6 85.6 80.4 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 94.7 REMARK 620 3 HIS B 374 NE2 90.7 93.5 REMARK 620 4 OGA B 502 O2' 91.3 171.9 81.0 REMARK 620 5 OGA B 502 O1 95.8 107.9 156.9 76.7 REMARK 620 6 HOH B 612 O 179.4 85.8 89.0 88.2 84.3 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 OGA 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 OGA 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 REMARK 900 RELATED ID: 5L9B RELATED DB: PDB DBREF 5L9V A 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 DBREF 5L9V B 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 DBREF 5L9V C 395 413 UNP Q16665 HIF1A_HUMAN 395 413 DBREF 5L9V D 395 413 UNP Q16665 HIF1A_HUMAN 395 413 SEQADV 5L9V GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V SER A 180 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V ALA A 201 UNP Q9GZT9 CYS 201 ENGINEERED MUTATION SEQADV 5L9V CYS A 281 UNP Q9GZT9 ARG 281 ENGINEERED MUTATION SEQADV 5L9V CYS A 317 UNP Q9GZT9 PRO 317 ENGINEERED MUTATION SEQADV 5L9V ALA A 398 UNP Q9GZT9 ARG 398 ENGINEERED MUTATION SEQADV 5L9V GLY B 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V SER B 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V HIS B 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V MET B 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V ALA B 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V SER B 180 UNP Q9GZT9 EXPRESSION TAG SEQADV 5L9V ALA B 201 UNP Q9GZT9 CYS 201 ENGINEERED MUTATION SEQADV 5L9V CYS B 281 UNP Q9GZT9 ARG 281 ENGINEERED MUTATION SEQADV 5L9V CYS B 317 UNP Q9GZT9 PRO 317 ENGINEERED MUTATION SEQADV 5L9V ALA B 398 UNP Q9GZT9 ARG 398 ENGINEERED MUTATION SEQADV 5L9V CYS C 397 UNP Q16665 LEU 397 ENGINEERED MUTATION SEQADV 5L9V CYS C 412 UNP Q16665 ASP 412 ENGINEERED MUTATION SEQADV 5L9V CYS D 397 UNP Q16665 LEU 397 ENGINEERED MUTATION SEQADV 5L9V CYS D 412 UNP Q16665 ASP 412 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 CYS 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 CYS 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 CYS 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 CYS 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 ALA CYS THR LEU LEU ALA PRO ALA ALA GLY ASP THR SEQRES 2 C 19 ILE ILE SER LEU CYS PHE SEQRES 1 D 19 ASP ALA CYS THR LEU LEU ALA PRO ALA ALA GLY ASP THR SEQRES 2 D 19 ILE ILE SER LEU CYS PHE HET MN A 501 1 HET OGA A 502 13 HET MN B 501 1 HET OGA B 502 13 HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE FORMUL 5 MN 2(MN 2+) FORMUL 6 OGA 2(C4 H5 N O5) FORMUL 9 HOH *224(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 CYS A 266 ASN A 284 1 19 HELIX 5 AA5 ASP A 335 GLY A 340 1 6 HELIX 6 AA6 ALA A 393 TYR A 403 1 11 HELIX 7 AA7 ALA B 190 TYR B 197 1 8 HELIX 8 AA8 TYR B 197 GLY B 206 1 10 HELIX 9 AA9 GLY B 215 THR B 232 1 18 HELIX 10 AB1 CYS B 266 ASN B 284 1 19 HELIX 11 AB2 ASP B 335 GLY B 340 1 6 HELIX 12 AB3 ALA B 393 VAL B 401 1 9 HELIX 13 AB4 ALA C 396 ALA C 401 1 6 HELIX 14 AB5 ALA D 396 LEU D 400 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 THR A 382 ASP A 392 -1 O ILE A 386 N TYR A 328 SHEET 5 AA1 7 ALA A 298 PRO A 304 -1 N MET A 299 O THR A 387 SHEET 6 AA1 7 LYS A 255 ILE A 259 -1 N THR A 257 O VAL A 300 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 THR A 382 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 ILE C 409 SER C 410 -1 O ILE C 409 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 ALA A 379 N THR A 308 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 ARG B 362 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 ARG B 362 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 ILE D 409 SER D 410 -1 O ILE D 409 N ARG B 295 SHEET 1 AA6 4 THR B 308 HIS B 313 0 SHEET 2 AA6 4 HIS B 374 ALA B 379 -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 SSBOND 1 CYS A 281 CYS C 412 1555 1555 2.04 SSBOND 2 CYS A 317 CYS C 397 1555 1555 2.04 SSBOND 3 CYS B 281 CYS D 412 1555 1555 2.04 SSBOND 4 CYS B 317 CYS D 397 1555 1555 2.03 LINK NE2 HIS A 313 MN MN A 501 1555 1555 2.18 LINK OD1 ASP A 315 MN MN A 501 1555 1555 2.25 LINK NE2 HIS A 374 MN MN A 501 1555 1555 2.19 LINK MN MN A 501 O2 OGA A 502 1555 1555 2.35 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.17 LINK MN MN A 501 O HOH A 626 1555 1555 2.30 LINK NE2 HIS B 313 MN MN B 501 1555 1555 2.22 LINK OD1 ASP B 315 MN MN B 501 1555 1555 2.16 LINK NE2 HIS B 374 MN MN B 501 1555 1555 2.14 LINK MN MN B 501 O2' OGA B 502 1555 1555 2.29 LINK MN MN B 501 O1 OGA B 502 1555 1555 2.22 LINK MN MN B 501 O HOH B 612 1555 1555 2.36 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 OGA A 502 SITE 2 AC1 5 HOH A 626 SITE 1 AC2 15 MET A 299 TYR A 310 HIS A 313 ASP A 315 SITE 2 AC2 15 TYR A 329 LEU A 343 HIS A 374 VAL A 376 SITE 3 AC2 15 ARG A 383 MN A 501 HOH A 606 HOH A 616 SITE 4 AC2 15 HOH A 626 HOH A 636 PRO C 402 SITE 1 AC3 5 HIS B 313 ASP B 315 HIS B 374 OGA B 502 SITE 2 AC3 5 HOH B 612 SITE 1 AC4 14 MET B 299 TYR B 310 HIS B 313 ASP B 315 SITE 2 AC4 14 TYR B 329 HIS B 374 VAL B 376 ARG B 383 SITE 3 AC4 14 MN B 501 HOH B 612 HOH B 615 HOH B 618 SITE 4 AC4 14 HOH B 654 PRO D 402 CRYST1 43.807 73.088 70.407 90.00 91.17 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 0.022827 0.000000 0.000467 0.00000 SCALE2 0.000000 0.013682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014206 0.00000