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 :  AQUO-MET STRUCTURE OF C.LACTEUS MINI-HB
 
Authors :  A. Pesce, M. Nardini, S. Dewilde, L. Capece, M. A. Marti, S. Congia, M. D. G. C. Blouin, D. A. Estrin, P. Ascenzi, L. Moens, M. Bolognesi, J. S. Ols
Date :  08 Jul 10  (Deposition) - 08 Dec 10  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxygen Storage, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Pesce, M. Nardini, S. Dewilde, L. Capece, M. A. Marti, S. Congia, M. D. Salter, G. C. Blouin, D. A. Estrin, P. Ascenzi, L. Moens, M. Bolognesi, J. S. Olson
Ligand Migration In The Apolar Tunnel Of Cerebratulus Lacteus Mini-Hemoglobin.
J. Biol. Chem. V. 286 5347 2011
PubMed-ID: 21147768  |  Reference-DOI: 10.1074/JBC.M110.169045

(-) Compounds

Molecule 1 - NEURAL HEMOGLOBIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonMILKY RIBBON-WORM
    Organism ScientificCEREBRATULUS LACTEUS
    Organism Taxid6221
    SynonymNRHB, MINI-HEMOGLOBIN
    TissueNERVE TISSUE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:0 , PHE A:10 , TYR A:21 , LYS A:24 , PHE A:25 , GLN A:44 , LYS A:47 , LEU A:65 , ARG A:68 , HIS A:69 , ARG A:72 , PHE A:79 , ILE A:102 , SO4 A:1111 , HOH A:2037 , HOH A:2060 , HOH A:2127 , HOH A:2128 , HOH A:2130 , HOH A:2131BINDING SITE FOR RESIDUE HEM A1110
2AC2SOFTWAREMET A:0 , VAL A:1 , TRP A:3 , ARG A:68 , HEM A:1110 , HOH A:2072 , HOH A:2133 , HOH A:2134 , HOH A:2135 , HOH A:2136 , HOH A:2137BINDING SITE FOR RESIDUE SO4 A1111
3AC3SOFTWAREASN A:2 , HIS A:93 , HOH A:2004BINDING SITE FOR RESIDUE GOL A1112

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XKI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XKI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XKI)

(-) Exons   (0, 0)

(no "Exon" information available for 2XKI)

(-) 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:110
 aligned with GLBN_CERLA | O76242 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
           GLBN_CERLA     1 MVNWAAVVDDFYQELFKAHPEYQNKFGFKGVALGSLKGNAAYKTQAGKTVDYINAAIGGSADAAGLASRHKGRNVGSAEFHNAKACLAKACSAHGAPDLGHAIDDILSHL 110
               SCOP domains d2xkia_ A: Nerve tissue mini-hemoglobin (neural globin)                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Globin-2xkiA01 A:1-87                                                                  ---------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2xki A   0 MVNWAAVVDDFYQELFKAHPEYQNKFGFKGVALGSLKGNAAYKTQAGKTVDYINAAIGGSADAAGLASRHKGRNVGSAEFHNAKACLAKACSAHGAPDLGHAIDDILSHL 109
                                     9        19        29        39        49        59        69        79        89        99       109

   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  (0, 0)

(no "CATH Domain" information available for 2XKI)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLBN_CERLA | O76242)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    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: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.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xki)
 

(-) 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
  2xki
    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
  GLBN_CERLA | O76242
    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
  GLBN_CERLA | O76242
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GLBN_CERLA | O762421kr7 1v07 2vyy 2vyz 2xkg 2xkh 4avd 4ave 4f68 4f69 4f6b 4f6d 4f6f 4f6g 4f6i 4f6j

(-) Related Entries Specified in the PDB File

1kr7 CRYSTAL STRUCTURE OF THE NERVE TISSUE MINI- HEMOGLOBIN FROMTHE NEMERTEAN WORM CEREBRATULUS LACTEUS
1v07 CRYSTAL STRUCTURE OF THRE11VAL MUTANT OF THE NERVE TISSUE MINI-HEMOGLOBIN FROM THE NEMERTEAN WORM CEREBRATULUS LACTEUS
2vyy MUTANT ALA55TRP OF CEREBRATULS LACTEUS MINI- HEMOGLOBIN
2vyz MUTANT ALA55PHE OF CEREBRATULUS LACTEUS MINI- HEMOGLOBIN
2xkg C.LACTEUS MINI-HB LEU86ALA MUTANT
2xkh XE DERIVATIVE OF C.LACTEUS MINI-HB LEU86ALA MUTANT