PDB Short entry for 5LA9 HEADER OXIDOREDUCTASE 14-JUN-16 5LA9 TITLE HIF PROLYL HYDROXYLASE 2 (PHD2-R281C/V314C) CROSS-LINKED TO HIF-1ALPHA TITLE 2 NODD-L397C/D412C AND N-OXALYLGLYCINE (NOG) (COMPLEX-2) 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 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; SOURCE 15 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 3 10-JAN-24 5LA9 1 LINK REVDAT 2 07-SEP-16 5LA9 1 JRNL REVDAT 1 31-AUG-16 5LA9 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. 2.81 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 15094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 717 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 48.1360 - 4.8092 0.99 3066 144 0.2194 0.2343 REMARK 3 2 4.8092 - 3.8177 0.96 2806 144 0.2185 0.2375 REMARK 3 3 3.8177 - 3.3353 0.98 2853 153 0.2580 0.2874 REMARK 3 4 3.3353 - 3.0304 0.99 2890 149 0.2990 0.3652 REMARK 3 5 3.0304 - 2.8132 0.96 2762 127 0.3321 0.3707 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 : 0.35 REMARK 3 B_SOL : 56.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 19.42000 REMARK 3 B22 (A**2) : -4.43000 REMARK 3 B33 (A**2) : -14.98000 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 : 0.003 3532 REMARK 3 ANGLE : 0.612 4799 REMARK 3 CHIRALITY : 0.044 523 REMARK 3 PLANARITY : 0.004 630 REMARK 3 DIHEDRAL : 15.175 2065 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 5LA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000395. 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 : 15152 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 48.129 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.24500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.7769 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 1.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.738 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 (%): 59.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 2.0 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 44.23350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.66450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.23350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.66450 REMARK 290 SMTRY3 4 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: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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: 2850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 SER A 242 REMARK 465 GLN A 243 REMARK 465 LYS A 244 REMARK 465 SER A 245 REMARK 465 ASP A 246 REMARK 465 SER A 247 REMARK 465 SER A 248 REMARK 465 LYS A 249 REMARK 465 ASP A 250 REMARK 465 LYS A 402 REMARK 465 TYR A 403 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 SER B 242 REMARK 465 GLN B 243 REMARK 465 LYS B 244 REMARK 465 SER B 245 REMARK 465 ASP B 246 REMARK 465 SER B 247 REMARK 465 SER B 248 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 LEU A 188 CG CD1 CD2 REMARK 470 LYS A 192 CG CD CE NZ REMARK 470 LEU A 195 CG CD1 CD2 REMARK 470 LYS A 204 CE NZ REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 GLN A 221 CG CD OE1 NE2 REMARK 470 LYS A 234 NZ REMARK 470 VAL A 241 CG1 CG2 REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 ILE A 256 CD1 REMARK 470 GLU A 260 CG CD OE1 OE2 REMARK 470 LYS A 262 CG CD CE NZ REMARK 470 LYS A 286 CD CE NZ REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 337 CG CD CE NZ REMARK 470 LYS A 350 CG CD CE NZ REMARK 470 LYS A 400 CE NZ REMARK 470 LEU B 188 CG CD1 CD2 REMARK 470 LEU B 191 CG CD1 CD2 REMARK 470 LYS B 192 CE NZ REMARK 470 GLU B 196 CD OE1 OE2 REMARK 470 LYS B 249 CG CD CE NZ REMARK 470 ASP B 250 CG OD1 OD2 REMARK 470 GLU B 260 CG CD OE1 OE2 REMARK 470 LYS B 262 CG CD CE NZ REMARK 470 LYS B 337 CE NZ REMARK 470 LYS B 350 CG CD CE NZ REMARK 470 GLN B 352 CG CD OE1 NE2 REMARK 470 LYS B 359 CE NZ REMARK 470 LYS B 402 CG CD CE NZ REMARK 470 TYR B 403 CG CD1 CD2 CE1 CE2 CZ OH 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 H ASP A 315 O HOH A 601 1.37 REMARK 500 MN MN B 501 O2' OGA B 502 1.68 REMARK 500 N ASP A 315 O HOH A 601 2.15 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 ALA A 194 -71.24 -57.98 REMARK 500 TYR A 197 -57.70 -132.29 REMARK 500 ASP A 212 60.22 61.65 REMARK 500 ASN A 284 137.85 -38.22 REMARK 500 ASP A 369 -160.61 -79.07 REMARK 500 TYR B 197 -54.90 -135.18 REMARK 500 ILE B 251 -72.47 -76.65 REMARK 500 ASP B 333 19.95 58.20 REMARK 500 PHE B 346 76.58 -118.70 REMARK 500 GLN B 352 -132.16 59.09 REMARK 500 ARG B 370 -4.68 -59.53 REMARK 500 CYS C 412 -34.99 67.26 REMARK 500 LEU D 400 40.28 -87.84 REMARK 500 CYS D 412 -103.51 46.07 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 96.7 REMARK 620 3 HIS A 374 NE2 90.8 96.0 REMARK 620 4 OGA A 502 O2 93.4 98.0 164.8 REMARK 620 5 OGA A 502 O2' 93.4 169.3 87.3 77.9 REMARK 620 6 HOH A 608 O 167.6 88.5 77.4 97.1 82.4 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 83.8 REMARK 620 3 HIS B 374 NE2 83.4 79.2 REMARK 620 4 OGA B 502 O1 86.7 105.9 168.3 REMARK 620 5 HOH B 606 O 153.8 78.0 74.8 116.4 REMARK 620 N 1 2 3 4 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 SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 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 REMARK 900 RELATED ID: 5L9V RELATED DB: PDB DBREF 5LA9 A 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 DBREF 5LA9 B 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 DBREF 5LA9 C 395 413 UNP Q16665 HIF1A_HUMAN 395 413 DBREF 5LA9 D 395 413 UNP Q16665 HIF1A_HUMAN 395 413 SEQADV 5LA9 GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 SER A 180 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 ALA A 201 UNP Q9GZT9 CYS 201 ENGINEERED MUTATION SEQADV 5LA9 CYS A 281 UNP Q9GZT9 ARG 281 ENGINEERED MUTATION SEQADV 5LA9 CYS A 314 UNP Q9GZT9 VAL 314 ENGINEERED MUTATION SEQADV 5LA9 ALA A 398 UNP Q9GZT9 ARG 398 ENGINEERED MUTATION SEQADV 5LA9 GLY B 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 SER B 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 HIS B 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 MET B 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 ALA B 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 SER B 180 UNP Q9GZT9 EXPRESSION TAG SEQADV 5LA9 ALA B 201 UNP Q9GZT9 CYS 201 ENGINEERED MUTATION SEQADV 5LA9 CYS B 281 UNP Q9GZT9 ARG 281 ENGINEERED MUTATION SEQADV 5LA9 CYS B 314 UNP Q9GZT9 VAL 314 ENGINEERED MUTATION SEQADV 5LA9 ALA B 398 UNP Q9GZT9 ARG 398 ENGINEERED MUTATION SEQADV 5LA9 CYS C 397 UNP Q16665 LEU 397 ENGINEERED MUTATION SEQADV 5LA9 CYS C 412 UNP Q16665 ASP 412 ENGINEERED MUTATION SEQADV 5LA9 CYS D 397 UNP Q16665 LEU 397 ENGINEERED MUTATION SEQADV 5LA9 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 CYS 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 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 CYS 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 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 SO4 A 503 5 HET MN B 501 1 HET OGA B 502 13 HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM SO4 SULFATE ION FORMUL 5 MN 2(MN 2+) FORMUL 6 OGA 2(C4 H5 N O5) FORMUL 7 SO4 O4 S 2- FORMUL 10 HOH *74(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 GLY A 233 1 19 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 VAL A 401 1 9 HELIX 7 AA7 PRO B 189 TYR B 197 1 9 HELIX 8 AA8 TYR B 197 HIS B 205 1 9 HELIX 9 AA9 LEU B 214 GLY B 233 1 20 HELIX 10 AB1 CYS B 266 ASN B 284 1 19 HELIX 11 AB2 ALA B 393 GLY B 406 1 14 SHEET 1 AA1 7 ILE A 207 ASP A 211 0 SHEET 2 AA1 7 ARG A 362 TRP A 367 -1 O PHE A 365 N CYS A 208 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 ALA A 301 O ALA A 385 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 ASP A 211 0 SHEET 2 AA2 6 ARG A 362 TRP A 367 -1 O PHE A 365 N CYS A 208 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 THR A 296 -1 N THR A 296 O TRP A 389 SHEET 6 AA2 6 ILE C 408 SER C 410 -1 O ILE C 409 N ARG A 295 SHEET 1 AA3 4 TYR A 310 HIS A 313 0 SHEET 2 AA3 4 HIS A 374 VAL A 376 -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 ALA A 354 N ILE A 345 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 TYR B 329 O ARG B 362 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 TYR B 329 O ARG B 362 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 ASN B 293 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 HIS B 374 N HIS B 313 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 ILE B 356 N LEU B 343 SSBOND 1 CYS A 281 CYS C 412 1555 1555 2.04 SSBOND 2 CYS A 314 CYS C 397 1555 1555 2.04 SSBOND 3 CYS B 281 CYS D 412 1555 1555 2.03 SSBOND 4 CYS B 314 CYS D 397 1555 1555 2.03 LINK NE2 HIS A 313 MN MN A 501 1555 1555 2.07 LINK OD1 ASP A 315 MN MN A 501 1555 1555 2.17 LINK NE2 HIS A 374 MN MN A 501 1555 1555 2.05 LINK MN MN A 501 O2 OGA A 502 1555 1555 2.35 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.06 LINK MN MN A 501 O HOH A 608 1555 1555 2.08 LINK NE2 HIS B 313 MN MN B 501 1555 1555 2.25 LINK OD1 ASP B 315 MN MN B 501 1555 1555 2.58 LINK NE2 HIS B 374 MN MN B 501 1555 1555 2.12 LINK MN MN B 501 O1 OGA B 502 1555 1555 2.17 LINK MN MN B 501 O HOH B 606 1555 1555 2.05 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 OGA A 502 SITE 2 AC1 5 HOH A 608 SITE 1 AC2 13 MET A 299 TYR A 310 HIS A 313 ASP A 315 SITE 2 AC2 13 TYR A 329 LEU A 343 HIS A 374 VAL A 376 SITE 3 AC2 13 ARG A 383 MN A 501 HOH A 608 HOH A 611 SITE 4 AC2 13 PRO C 402 SITE 1 AC3 1 ARG A 396 SITE 1 AC4 5 HIS B 313 ASP B 315 HIS B 374 OGA B 502 SITE 2 AC4 5 HOH B 606 SITE 1 AC5 10 TYR B 310 HIS B 313 TYR B 329 HIS B 374 SITE 2 AC5 10 VAL B 376 ARG B 383 MN B 501 HOH B 606 SITE 3 AC5 10 HOH B 621 PRO D 402 CRYST1 88.467 97.329 71.001 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011304 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010274 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014084 0.00000