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 :  CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT
 
Authors :  M. A. Hough, S. V. Antonyuk, S. S. Hasnain
Date :  22 Jul 10  (Deposition) - 10 Nov 10  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Haemoprotein, 4-Helix Bundle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Hough, S. V. Antonyuk, S. Barbieri, N. Rustage, A. L. Mckay, A. E. Servid, R. R. Eady, C. R. Andrew, S. S. Hasnain
Distal-To-Proximal No Conversion In Hemoproteins: The Role Of The Proximal Pocket.
J. Mol. Biol. V. 405 395 2011
PubMed-ID: 21073879  |  Reference-DOI: 10.1016/J.JMB.2010.10.035

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1HEC2Ligand/IonHEME C
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , LEU A:16 , THR A:17 , MET A:19 , ALA A:20 , TRP A:56 , GLY A:65 , ASP A:67 , ILE A:72 , GLN A:83 , PHE A:86 , CYS A:116 , CYS A:119 , HIS A:120 , TYR A:123 , LYS A:124 , HOH A:2011 , HOH A:2116BINDING SITE FOR RESIDUE HEC A1128

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XM0)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_ALCXX7-125  1A:7-125
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_ALCXX7-125  2A:7-125

(-) Exons   (0, 0)

(no "Exon" information available for 2XM0)

(-) 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:125
 aligned with CYCP_ALCXX | P00138 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           CYCP_ALCXX     1 QFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRK 125
               SCOP domains d2xm0a_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Cytochrom_C_2-2xm0A01 A:6-124                                                                                          - Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: A:7-125 UniProt: 7-125                                                                                     PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xm0 A   1 xFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYKK 125
                            |       10        20        30        40        50        60        70        80        90       100       110       120     
                            |                                                                                                                            
                            1-PCA
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XM0)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Cytochrom_C_2] (14)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (CYCP_ALCXX | P00138)
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: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.
biological process
    GO:0022900    electron transport chain    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: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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    HEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xm0)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2xm0
    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
  CYCP_ALCXX | P00138
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  CYCP_ALCXX | P00138
    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
        CYCP_ALCXX | P00138: 1cgn 1cgo 1e83 1e84 1e85 1e86 2xl6 2xl8 2xld 2xle 2xlh 2xlm 2xlo 2xlv 2xlw 2xm4 2ykz 2yl0 2yl1 2yl3 2yl7 2yld 2ylg 2yli 3zqv 3zqy 3ztm 3ztz 3zwi 4cda 4cdv 4cdy 4cip 4cjg 4cjo 4d4n 4d4x 4wgy 4wgz 5agf 5jli 5jp7 5jra 5js5 5jsl 5jt4 5jua 5jve

(-) Related Entries Specified in the PDB File

1cgn CYTOCHROME C'
1cgo CYTOCHROME C'
1e83 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - OXIDIZED STRUCTURE
1e84 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE
1e85 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE WITH NO BOUND TO PROXIMAL SIDE OF HEME
1e86 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE WITH CO BOUND TO DISTAL SIDE OF HEME
2xl5 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT
2xl6 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124A VARIANT WITH BOUND NO
2xl8 REDUCED STRUCTURE OF R124F MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS
2xld CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q VARIANT
2xle CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT WITH BOUND NO
2xlh REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS
2xlm CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS RECOMBINANT NATIVE WITH BOUND NO
2xlo CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E VARIANT WITH BOUND NO
2xlv CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124F VARIANT WITH BOUND NO
2xlw CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q VARIANT WITH BOUND NO
2xlx CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K VARIANT
2xm4 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E VARIANT