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(-) Description

Title :  HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) R371H VARIANT IN COMPLEX WITH MN(II) AND N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE (IOX3/UN9)
 
Authors :  R. Chowdhury, C. J. Schofield
Date :  15 Jun 16  (Deposition) - 31 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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
    ChainsA
    EC Number1.14.11.29
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A(+)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, UNP RESIDUES 181-426
    GeneEGLN1, C1ORF12, PNAS-118, PNAS-137
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHYPOXIA-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  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MN1Ligand/IonMANGANESE (II) ION
3SO41Ligand/IonSULFATE ION
4UN91Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , UN9 A:502 , HOH A:623binding site for residue MN A 501
2AC2SOFTWAREASP A:254 , MET A:299 , TYR A:303 , 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:623 , HOH A:636binding site for residue UN9 A 502
3AC3SOFTWAREARG A:396binding site for residue SO4 A 503
4AC4SOFTWARELYS A:262 , ARG A:312 , PRO A:373binding site for residue GOL A 504

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:201 -A:208

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LB6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5LB6)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh.......eee...hhhhhee..eeeee......hhhhhhhhhhhhhhhhhh........eeee..eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eee......eeeeeeeeeehhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lb6 A 188 LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRHNPHEVQPAYATRYAITVWYFDADERARAKVKYLKGVR 411
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397      |410 
                                                                                                                                                                                                                                                  404|   
                                                                                                                                                                                                                                                   408   

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LB6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LB6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LB6)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        EGLN1_HUMAN | Q9GZT92g19 2g1m 2hbt 2hbu 2y33 2y34 3hqr 3hqu 3ouh 3oui 3ouj 4bqw 4bqx 4bqy 4jzr 4kbz 4uwd 5a3u 5l9b 5l9r 5l9v 5la9 5las 5lat 5lbb 5lbc 5lbe 5lbf 5v18

(-) Related Entries Specified in the PDB File

3hqr 4bqx 5l9b 5l9r 5l9v 5la9 5las 5lat