Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 6-(5-OXO-4-(1H-1,2,3-TRIAZOL-1-YL)-2,5-DIHYDRO-1H-PYRAZOL-1-YL) NICOTINIC ACID
 
Authors :  R. Chowdhury, V. Gomez-Perez, C. J. Schofield
Date :  03 Jun 15  (Deposition) - 17 Jun 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Oxidoreductase, Non-Heme, Iron, 2-Oxoglutarate, Dioxygenase, Hypoxia-Inducible Factor, Hif, Hif Prolyl Hydroxylase Domain 2, Phd2, Egln, Oxygenase, Hypoxia, Dna-Binding, Metal-Binding, Transcription, Helix-Loop-Helix-Beta, Dsbh, Facial Triad, Asparaginyl/ Aspartyl Hydroxylase, Transcription And Epigenetic Regulation, Signaling, Development, Cell Structure, Ankyrin Repeat Domain, Ard, Beta-Hydroxylation, Transcription Activator/Inhibitor, Phosphorylation, S-Nitrosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Chan, O. Atasoylu, E. Hodson, A. Tumber, I. K. H. Leung, R. Chowdhury, V. Gomez-Perez, M. Demetriades, A. M. Rydzik, J. Holt-Martyn, Y. Tian, T. Bishop, T. D. W. Claridge, A. Kawamura, C. W. Pugh, P. J. Ratcliffe, C. J. Schofield
Potent And Selective Triazole-Based Inhibitors Of The Hypoxia-Inducible Factor Prolyl-Hydroxylases With Activity In The Murine Brain.
Plos One V. 10 32004 2015
PubMed-ID: 26147748  |  Reference-DOI: 10.1371/JOURNAL.PONE.0132004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EGL NINE HOMOLOG 1
    Chains: A, B, C
    EC Number: 1.14.11.2, 1.14.11.29, 1.14.11.-
    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
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2, HIF-PH2, HIF-PROLYL HYDROXYLASE 2, HPH-2, PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2, PHD2, SM-20, HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION
2R8J3Ligand/Ion6-(5-OXO-4-(1H-1,2,3-TRIAZOL-1-YL)-2,5-DIHYDRO-1H-PYRAZOL-1-YL)NICOTINIC ACID
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2R8J6Ligand/Ion6-(5-OXO-4-(1H-1,2,3-TRIAZOL-1-YL)-2,5-DIHYDRO-1H-PYRAZOL-1-YL)NICOTINIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , R8J A:1421BINDING SITE FOR RESIDUE MN A1420
2AC2SOFTWARETYR A:303 , HIS A:313 , ASP A:315 , ARG A:322 , HIS A:374 , ARG A:383 , TRP A:389 , MN A:1420BINDING SITE FOR RESIDUE R8J A1421
3AC3SOFTWAREHIS B:313 , ASP B:315 , HIS B:374 , R8J B:1406BINDING SITE FOR RESIDUE MN B1405
4AC4SOFTWARETYR B:303 , HIS B:313 , ASP B:315 , ARG B:322 , HIS B:374 , ARG B:383 , TRP B:389 , MN B:1405BINDING SITE FOR RESIDUE R8J B1406
5AC5SOFTWAREHIS C:313 , ASP C:315 , HIS C:374 , R8J C:1407BINDING SITE FOR RESIDUE MN C1406
6AC6SOFTWARETYR C:303 , HIS C:313 , ASP C:315 , ARG C:322 , ILE C:327 , ARG C:383 , TRP C:389 , MN C:1406BINDING SITE FOR RESIDUE R8J C1407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A3U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A3U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A3U)

(-) Exons   (0, 0)

(no "Exon" information available for 5A3U)

(-) 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
(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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhheeeee..hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhh....eeee..eeeeee....eeeeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eeeeee...eeeeeeeeeehhhhhhhhhhh......ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a3u A 184 QTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELNKPSD 419
                                   193       203       213       223       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414     
                                                                          232|                                                                                                                                                                     
                                                                           254                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhhhh.........eeee..eeeeee......eeee........eeeeeeee.............eee......eeeee.....eeeeee......eee......eeeeeeeeeehhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a3u B 188 LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYL 404
                                   197       207       217       227       237|      262       272       282       292       302       312       322       332       342       352       362       372       382       392       402  
                                                                           237|                                                                                                                                                       
                                                                            253                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh........eeee..eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eee......eeeeeeeeeehhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a3u C 188 LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLT 405
                                   197       207       217       227    || 256       266       276       286       296       306       316       326       336       346       356       366       376       386       396         
                                                                      232|                                                                                                                                                         
                                                                       252
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5A3U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A3U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A3U)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    R8J  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a3u)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5a3u
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EGLN1_HUMAN | Q9GZT9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.11.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.14.11.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.14.11.29
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  EGLN1_HUMAN | Q9GZT9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 5l9b 5l9r 5l9v 5la9 5las 5lat 5lb6 5lbb 5lbc 5lbe 5lbf 5v18

(-) Related Entries Specified in the PDB File

2g19 CELLULAR OXYGEN SENSING: CRYSTAL STRUCTURE OF HYPOXIA- INDUCIBLE FACTOR PROLYL HYDROXYLASE (PHD2)
2g1m CELLULAR OXYGEN SENSING: CRYSTAL STRUCTURE OF HYPOXIA- INDUCIBLE FACTOR PROLYL HYDROXYLASE (PHD2)
4bqw HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH MN(II) AND 2-(4-HYDROXY-2-OXO-1,2- DIHYDROQUINOLINE-3-CARBOXAMIDO)ACETIC ACID
4bqx HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH MN(II) AND N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL )CARBONYL]GLYCINE (IOX3/UN9)
4bqy HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH FE(II) AND N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL )CARBONYL]ALANINE