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(-) Description

Title :  HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) R396T 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. Unit :  A
Biol. Unit 1:  A  (3x)
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 BL21(DE3)
    Expression System Plasmid: PET28A(+)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP 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 Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1BCT1Ligand/IonBICARBONATE ION
2MN1Ligand/IonMANGANESE (II) ION
3UN91Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1BCT3Ligand/IonBICARBONATE ION
2MN-1Ligand/IonMANGANESE (II) ION
3UN93Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , UN9 A:502 , HOH A:641binding site for residue MN A 501
2AC2SOFTWAREASP A:254 , ILE A:256 , 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 , ARG A:398 , MN A:501 , HOH A:631 , HOH A:641binding site for residue UN9 A 502
3AC3SOFTWARELYS A:262 , ARG A:312 , PRO A:373binding site for residue BCT A 503

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhhhhh.......eee........ee..eeeee......hhhhhhhhhhhhhhhhhh........eeee..eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee......eeeee......eee......eeeeeeeeeehhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lbb A 182 NGQTLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADETARAKVKYLTGGVRVEL 414
                               ||  193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403  ||     
                             185|                                                                                                                                                                                                                       406|     
                              188                                                                                                                                                                                                                        409
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  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 5LBB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

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  5lbb
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  EGLN1_HUMAN | Q9GZT9
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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 5l9r 5l9v 5la9 5las 5lat 5lb6 5lbc 5lbe 5lbf 5v18

(-) Related Entries Specified in the PDB File

3hqr 4bqx 5l9b 5l9r 5l9v 5la9 5las 5lat 5lb6