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 :  STRUCTURE OF FACTOR INHIBITING HIF (FIH) IN COMPLEX WITH FE, NO, AND NOG
 
Authors :  C. Y. Taabazuing, S. C. Garman, M. J. Knapp
Date :  27 Mar 15  (Deposition) - 13 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hypoxia Inducible Factor, Factor Inhibiting Hif, Hydroxylase, Oxygen Sensing, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Y. Taabazuing, J. Fermann, S. Garman, M. J. Knapp
Substrate Promotes Productive Gas Binding In The Alpha-Ketoglutarate-Dependent Oxygenase Fih.
Biochemistry V. 55 277 2016
PubMed-ID: 26727884  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01003

(-) Compounds

Molecule 1 - HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
    ChainsA
    EC Number1.14.11.30, 1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneHIF1AN, FIH1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFACTOR INHIBITING HIF-1,FIH-1,HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2NO1Ligand/IonNITRIC OXIDE
3OGA1Ligand/IonN-OXALYLGLYCINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NO-1Ligand/IonNITRIC OXIDE
3OGA2Ligand/IonN-OXALYLGLYCINE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO410Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:145 , LEU A:188 , THR A:196 , HIS A:199 , ASP A:201 , ASN A:205 , PHE A:207 , LYS A:214 , HIS A:279 , ILE A:281 , ASN A:294 , TRP A:296 , NO A:602 , PEG A:603 , FE A:604binding site for residue OGA A 601
2AC2SOFTWAREHIS A:199 , ASP A:201 , TRP A:296 , OGA A:601 , PEG A:603 , FE A:604binding site for residue NO A 602
3AC3SOFTWARETYR A:102 , GLN A:147 , LEU A:188 , ARG A:238 , OGA A:601 , NO A:602 , HOH A:755 , HOH A:771binding site for residue PEG A 603
4AC4SOFTWAREHIS A:199 , ASP A:201 , HIS A:279 , OGA A:601 , NO A:602binding site for residue FE A 604
5AC5SOFTWARELYS A:311 , ALA A:312 , HOH A:718 , HOH A:758binding site for residue SO4 A 605
6AC6SOFTWARELYS A:107 , GLU A:202 , ARG A:320 , LYS A:324binding site for residue SO4 A 606
7AC7SOFTWAREARG A:143 , GLU A:192 , GLY A:193 , LEU A:285 , ASN A:286binding site for residue SO4 A 607
8AC8SOFTWAREARG A:138 , GLY A:140 , GLU A:141 , GLU A:142binding site for residue SO4 A 608
9AC9SOFTWAREARG A:17 , ARG A:44binding site for residue SO4 A 609

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z1V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:308 -Pro A:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z1V)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z1V)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh....hhhhh......eee..ee...hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh...eeeeeee........hhhhhh..........eeeeehhhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhh.hhhhhhhhhhhh....eee.eeeee....eeeee....eeeeeeee..eeeeeehhhhhhhhh.......................hhhhhhh.eeeeee....eeee....eeeeee......eeeeeeee.............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z1v A   9 VASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348 

   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 4Z1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z1V)

(-) Gene Ontology  (32, 32)

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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:308 - Pro A:309   [ RasMol ]  
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4z1v
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HIF1N_HUMAN | Q9NWT6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.11.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
  1.14.11.30
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  HIF1N_HUMAN | Q9NWT6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HIF1N_HUMAN | Q9NWT61h2k 1h2l 1h2m 1h2n 1iz3 1mze 1mzf 1yci 2cgn 2cgo 2ilm 2w0x 2wa3 2wa4 2xum 2y0i 2yc0 2yde 3d8c 3kcx 3kcy 3od4 3p3n 3p3p 4ai8 4b7e 4b7k 4bio 4jaa 4nr1 4z2w 5jwk 5jwl 5jwp

(-) Related Entries Specified in the PDB File

4z2w