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

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOGLOBIN AT 1.68 ANGSTROMS RESOLUTION
 
Authors :  M. Makino, H. Sugimoto, H. Sawai, N. Kawada, K. Yoshizato, Y. Shiro, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  21 Dec 05  (Deposition) - 23 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytoglobin, Myoglobin, Heme, Oxygen Transport, Oxygen Storage, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Makino, H. Sugimoto, H. Sawai, N. Kawada, K. Yoshizato, Y. Shiro
High-Resolution Structure Of Human Cytoglobin: Identification Of Extra N- And C-Termini And A New Dimerization Mode.
Acta Crystallogr. , Sect. D V. 62 671 2006
PubMed-ID: 16699195  |  Reference-DOI: 10.1107/S0907444906013813
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOGLOBIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCYGB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainBACTERIA
    SynonymHISTOGLOBIN, HGB, STELLATE CELL ACTIVATION- ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:56 , TYR A:59 , PHE A:60 , GLN A:77 , HIS A:81 , ARG A:84 , VAL A:85 , HIS A:113 , HIS A:117 , VAL A:119 , TYR A:123 , PHE A:124 , HOH A:1212 , HOH A:1237 , HOH A:1314 , HOH A:1331 , HOH A:1340 , HOH A:1348BINDING SITE FOR RESIDUE HEM A 191
2AC2SOFTWAREALA B:56 , TYR B:59 , PHE B:60 , GLN B:77 , HIS B:81 , VAL B:85 , HIS B:113 , HIS B:117 , VAL B:119 , PHE B:124 , LEU B:127 , HOH B:206 , HOH B:219 , HOH B:223 , HOH B:226 , HOH B:286 , HOH B:296BINDING SITE FOR RESIDUE HEM B 191
3AC3SOFTWARETYR A:35 , CYS A:83 , GLY A:87 , HOH A:1211 , HOH A:1292 , TYR B:35 , CYS B:83 , GLY B:87BINDING SITE FOR RESIDUE ACY A 1200

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:38 -B:83
2A:83 -B:38

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:175 -Pro A:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DC3)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.CYGB_HUMAN19-158
 
  2A:19-158
B:19-158

(-) Exons   (4, 7)

Asymmetric/Biological Unit (4, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002932301ENSE00001246500chr17:74533966-74533482485CYGB_HUMAN1-48482A:17-48
B:4-48
32
45
1.2ENST000002932302ENSE00001058643chr17:74527773-74527542232CYGB_HUMAN48-125782A:48-125
B:48-125
78
78
1.3ENST000002932303ENSE00001118062chr17:74527224-74527061164CYGB_HUMAN126-180552A:126-180
B:126-171
55
46
1.4ENST000002932304ENSE00001193939chr17:74524693-745234611233CYGB_HUMAN180-190111A:180-188
-
9
-

(-) 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:172
 aligned with CYGB_HUMAN | Q8WWM9 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:172
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186  
           CYGB_HUMAN    17 EELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGWVQQVPNATTPPATLPSS 188
               SCOP domains d2dc3a_ A: Cytoglobin                                                                                                                                                        SCOP domains
               CATH domains 2dc3A00 A:17-188 Globins                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:19-158 UniProt: 19-158                                                                                                       ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:17-48          -----------------------------------------------------------------------------Exon 1.3  PDB: A:126-180 UniProt: 126-180              -------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.2  PDB: A:48-125 UniProt: 48-125                                       ------------------------------------------------------Exon 1.4  Transcript 1 (2)
                 2dc3 A  17 EELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGWVQQVPNATTPPATLPSS 188
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186  

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with CYGB_HUMAN | Q8WWM9 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:168
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        
           CYGB_HUMAN     4 VPGEMEIERRERSEELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
               SCOP domains d2dc3b_ B: Cytoglobin                                                                                                                                                    SCOP domains
               CATH domains 2dc3B00 B:4-171 Globins                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------GLOBIN  PDB: B:19-158 UniProt: 19-158                                                                                                       ------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:4-48 UniProt: 1-48          -----------------------------------------------------------------------------Exon 1.3  PDB: B:126-171 UniProt: 126-180      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.2  PDB: B:48-125 UniProt: 48-125                                       ---------------------------------------------- Transcript 1 (2)
                 2dc3 B   4 VPGEMEIERRERSEELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGW 171
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DC3)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CYGB_HUMAN | Q8WWM9)
molecular function
    GO:0004096    catalase activity    Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O.
    GO:0047888    fatty acid peroxidase activity    Catalysis of the reaction: 2 H(2)O(2) + H(+) + palmitate = CO(2) + 3 H(2)O + pentadecanal.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008941    nitric oxide dioxygenase activity    Catalysis of the reaction: 2 NO + 2 O2 + NADPH + H+ = 2 nitrate + NADP+.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0019395    fatty acid oxidation    The removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen.
    GO:0032966    negative regulation of collagen biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:0010764    negative regulation of fibroblast migration    Any process that decreases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
    GO:2000490    negative regulation of hepatic stellate cell activation    Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell activation.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0050999    regulation of nitric-oxide synthase activity    Any process that modulates the activity of the enzyme nitric-oxide synthase.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

 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
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:175 - Pro A:176   [ RasMol ]  
 

(-) 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
  2dc3
    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
  CYGB_HUMAN | Q8WWM9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  CYGB_HUMAN | Q8WWM9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CYGB_HUMAN | Q8WWM91umo 1urv 1ury 1ut0 1ux9 1v5h 3ag0 4b3w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DC3)