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 :  REDUCED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6
 
Authors :  I. Bento, R. Louro, P. M. Matias, T. Catarino, A. M. Baptista, C. M. Soare M. A. Carrondo, D. L. Turner, A. V. Xavier
Date :  12 Sep 01  (Deposition) - 12 Sep 02  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport, Cytochrome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Louro, I. Bento, P. M. Matias, T. Catarino, A. M. Baptista, C. M. Soares, M. A. Carrondo, D. L. Turner, A. V. Xavier
Conformational Component In The Coupled Transfer Of Multipl Electrons And Protons In A Monomeric Tetraheme Cytochrome
J. Biol. Chem. V. 276 44044 2001
PubMed-ID: 11551953  |  Reference-DOI: 10.1074/JBC.M107136200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C3
    Atcc: 27774
    Chains: A
    Organism Scientific: DESULFOVIBRIO DESULFURICANS
    Organism Taxid: 876

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1HEC4Ligand/IonHEME C
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:5 , ASP A:6 , LYS A:7 , PRO A:8 , PRO A:21 , HIS A:22 , ALA A:23 , PRO A:24 , LYS A:90 , HOH A:2023 , HOH A:2096BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWARELYS A:16 , THR A:17 , LYS A:85BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWAREPRO A:2 , PRO A:5 , GLU A:10 , PHE A:20 , HIS A:22 , HIS A:25 , CYS A:30 , CYS A:33 , HIS A:34 , TYR A:43 , ALA A:44 , LYS A:45 , CYS A:46 , HEC A:203 , HOH A:2092BINDING SITE FOR RESIDUE HEC A 201
4AC4SOFTWARECYS A:33 , HIS A:34 , HIS A:35 , ALA A:44 , LYS A:45 , CYS A:46 , CYS A:51 , HIS A:52 , GLU A:61 , GLU A:73 , LEU A:74 , LYS A:75 , HIS A:76 , HOH A:2042 , HOH A:2093BINDING SITE FOR RESIDUE HEC A 202
5AC5SOFTWAREGLU A:10 , PHE A:20 , HIS A:25 , CYS A:79 , CYS A:82 , HIS A:83 , GLU A:89 , LYS A:90 , LEU A:93 , LEU A:97 , LYS A:104 , HEC A:201BINDING SITE FOR RESIDUE HEC A 203
6AC6SOFTWAREVAL A:11 , GLY A:13 , SER A:14 , GLN A:15 , LYS A:16 , VAL A:18 , ASP A:38 , GLY A:39 , LEU A:55 , TYR A:65 , VAL A:68 , HIS A:69 , HIS A:83 , LEU A:97 , THR A:98 , GLY A:99 , CYS A:100 , CYS A:105 , HIS A:106 , HOH A:2095BINDING SITE FOR RESIDUE HEC A 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GMB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GMB)

(-) 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:107
 aligned with Q9L915_DESDE | Q9L915 from UniProtKB/TrEMBL  Length:128

    Alignment length:107
                                    31        41        51        61        71        81        91       101       111       121       
         Q9L915_DESDE    22 APAVPDKPVEVKGSQKTVMFPHAPHEKVECVTCHHLVDGKESYAKCGSSGCHDDLTAKKGEKSLYYVVHAKGELKHTSCLACHSKVVAEKPELKKDLTGCAKSKCHP 128
               SCOP domains d1gmba_ A: Cytochrome c3                                                                                    SCOP domains
               CATH domains 1gmbA00 A:1-107 Cytochrome C3                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....eeee.hhhhh..hhhhhh............................hhhhhhhh.......hhhhhhhhhhhhh..hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1gmb A   1 APAVPDKPVEVKGSQKTVMFPHAPHEKVECVTCHHLVDGKESYAKCGSSGCHDDLTAKKGEKSLYYVVHARGELKHTSCLACHSKVVAEKPELKKDLTGCAKSKCHP 107
                                    10        20        30        40        50        60        70        80        90       100
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9L915_DESDE | Q9L915)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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.

 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
    HEC  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gmb)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  1gmb
    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
  Q9L915_DESDE | Q9L915
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q9L915_DESDE | Q9L915
    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
        Q9L915_DESDE | Q9L915: 2kmy 2ksu
UniProtKB/TrEMBL
        Q9L915_DESDE | Q9L915: 1gm4 1i77 1up9 1upd 3cyr

(-) Related Entries Specified in the PDB File

1gm4 OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6
3cyr CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774P