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

(-) Description

Title :  HUMAN BILIVERDIN IX BETA REDUCTASE: NADP COMPLEX
 
Authors :  P. J. B. Pereira, S. Macedo-Ribeiro, A. Parraga, R. Perez-Luque, O. Cunningham, K. Darcy, T. J. Mantle, M. Coll
Date :  16 Nov 00  (Deposition) - 28 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Biliverdin-Ix Beta Reductase, Foetal Metabolism, Haem Degradation, Flavin Reductase, Diaphorase, Green Haem Binding Protein, Methaemoglobin Reductase, Alpha/Beta Dinucleotide Binding Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. J. B. Pereira, S. Macedo-Ribeiro, A. Parraga, R. Perez-Luque, O. Cunningham, K. Darcy, T. J. Mantle, M. Coll
Structure Of Human Biliverdin Ix Beta Reductase, An Early Fetal Bilirubin Ix Producing Enzyme
Nat. Struct. Biol. V. 8 215 2001
PubMed-ID: 11224564  |  Reference-DOI: 10.1038/84948

(-) Compounds

Molecule 1 - BILIVERDIN IX BETA REDUCTASE
    ChainsA
    EC Number1.3.1.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFLAVIN REDUCTASE (EC 1.6.99.1), NADPH-DEPENDENT DIAPHORASE, NADPH-FLAVIN REDUCTASE, BILIVERDIN REDUCTASE B, GREEN HEME BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , THR A:12 , GLY A:13 , GLN A:14 , THR A:15 , ARG A:35 , ARG A:39 , ASP A:54 , VAL A:55 , LEU A:74 , LEU A:75 , GLY A:76 , ARG A:78 , MET A:87 , CYS A:109 , THR A:110 , SER A:111 , HIS A:132 , PRO A:151 , PRO A:152 , HIS A:153 , ILE A:154 , HOH A:2076 , HOH A:2273 , HOH A:2347 , HOH A:2348 , HOH A:2349 , HOH A:2350 , HOH A:2351 , HOH A:2352 , HOH A:2353 , HOH A:2354 , HOH A:2355 , HOH A:2356 , HOH A:2357 , HOH A:2358 , HOH A:2359BINDING SITE FOR RESIDUE NAP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HDO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HDO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019168R46QBLVRB_HUMANPolymorphism11547746AR46Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HDO)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002633681ENSE00001504331chr19:40971725-40971517209BLVRB_HUMAN1-27271A:1-2727
1.2ENST000002633682ENSE00001504330chr19:40964452-40964288165BLVRB_HUMAN27-82561A:27-8256
1.3ENST000002633683ENSE00000706810chr19:40964151-4096406290BLVRB_HUMAN82-112311A:82-11231
1.4ENST000002633684ENSE00000706793chr19:40957399-40957271129BLVRB_HUMAN112-155441A:112-15544
1.5ENST000002633685ENSE00001139369chr19:40953953-40953693261BLVRB_HUMAN155-206521A:155-20551

(-) 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:205
 aligned with BLVRB_HUMAN | P30043 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
          BLVRB_HUMAN     1 MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQY 205
               SCOP domains d1hdoa_ A: Biliverdin IX beta reductase                                                                                                                                                                       SCOP domains
               CATH domains 1hdoA00 A:1-205 NAD(P)-binding Rossmann-like Domain                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhh........eeee....hhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhhhh..eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhh..eeeee...eee........eee........eeehhhhhhhhhhh.........eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-27      ------------------------------------------------------Exon 1.3  PDB: A:82-112        ------------------------------------------Exon 1.5  PDB: A:155-205 UniProt: 155-206           Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.2  PDB: A:27-82 UniProt: 27-82                   -----------------------------Exon 1.4  PDB: A:112-155 UniProt: 112-155   -------------------------------------------------- Transcript 1 (2)
                 1hdo A   1 MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQY 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HDO)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BLVRB_HUMAN | P30043)
molecular function
    GO:0004074    biliverdin reductase activity    Catalysis of the reaction: bilirubin + NAD(P)+ = biliverdin + NAD(P)H + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0042602    riboflavin reductase (NADPH) activity    Catalysis of the reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + 2 H+.
biological process
    GO:0042167    heme catabolic process    The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hdo)
 

(-) 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
  1hdo
    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
  BLVRB_HUMAN | P30043
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.3.1.24
    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
  BLVRB_HUMAN | P30043
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BLVRB_HUMAN | P300431he2 1he3 1he4 1he5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1HDO)