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(-) Description

Title :  HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG)
 
Authors :  R. Chowdhury, C. J. Schofield
Date :  10 Jun 16  (Deposition) - 31 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Non-Heme Dioxygenase, Iron, 2-Oxoglutarate, Hypoxia- Inducible Factor, Hif, Hif Prolyl Hydroxylase Domain 2, Phd2, Egln1, Oxygenase, Hypoxia, Dna-Binding, Metal-Binding, Transcription, Helix-Loop-Helix-Beta, Dsbh, Facial Triad, Cytoplasm, Transcription/Epigenetic Regulation, Signaling, Development, Cell Structure, Beta-Hydroxylation, Transcription Activator/Inhibitor, Ubl Conjugation, Polymorphism, Vitamin C, Zinc-Finger, Familial Erythrocytosis, Breast Cancer, Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Chowdhury, I. K. Leung, Y. M. Tian, M. I. Abboud, W. Ge, C. Domene, F. X. Cantrelle, I. Landrieu, A. P. Hardy, C. W. Pugh, P. J. Ratcliffe, T. D. Claridge, C. J. Schofield
Structural Basis For Oxygen Degradation Domain Selectivity Of The Hif Prolyl Hydroxylases.
Nat Commun V. 7 12673 2016
PubMed-ID: 27561929  |  Reference-DOI: 10.1038/NCOMMS12673
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EGL NINE HOMOLOG 1
    Chains: A
    EC Number: 1.14.11.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 181-426
    Gene: EGLN1, C1ORF12, PNAS-118, PNAS-137
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2,HPH-2,PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2,PHD2,SM-20

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MN1Ligand/IonMANGANESE (II) ION
3OGA2Ligand/IonN-OXALYLGLYCINE
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , OGA A:502 , HOH A:650binding site for residue MN A 501
2AC2SOFTWAREMET A:299 , TYR A:310 , HIS A:313 , ASP A:315 , TYR A:329 , LEU A:343 , HIS A:374 , VAL A:376 , ARG A:383 , MN A:501 , HOH A:613 , HOH A:622 , HOH A:626 , HOH A:647 , HOH A:650binding site for residue OGA A 502
3AC3SOFTWAREVAL A:209 , ASP A:355 , ILE A:356 , ARG A:362 , HOH A:603 , HOH A:620 , HOH A:641 , HOH A:675binding site for residue OGA A 503
4AC4SOFTWAREGLY A:294 , ARG A:295 , SO4 A:507 , HOH A:652 , HOH A:699binding site for residue PG4 A 504
5AC5SOFTWAREARG A:312 , HIS A:313 , VAL A:314 , PRO A:373 , HOH A:602 , HOH A:667binding site for residue SO4 A 505
6AC6SOFTWAREILE A:292 , HOH A:609 , HOH A:692binding site for residue SO4 A 506
7AC7SOFTWAREARG A:322 , PG4 A:504binding site for residue SO4 A 507
8AC8SOFTWAREARG A:252 , GLY A:253 , GLY A:309 , TYR A:310 , HOH A:610binding site for residue GOL A 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L9R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L9R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L9R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L9R)

(-) Exons   (0, 0)

(no "Exon" information available for 5L9R)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh...eehhhhhh...........eeeee......hhhhhhhhhhhhhhhhhhh.......eeee..eeeeeee...eeeeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eeeeee..eeeeeeeeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l9r A 185 TKPLPALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKVKYL 404
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5L9R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L9R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L9R)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EGLN1_HUMAN | Q9GZT9: 2g19 2g1m 2hbt 2hbu 2y33 2y34 3hqr 3hqu 3ouh 3oui 3ouj 4bqw 4bqx 4bqy 4jzr 4kbz 4uwd 5a3u 5l9b 5l9v 5la9 5las 5lat 5lb6 5lbb 5lbc 5lbe 5lbf 5v18

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L9R)