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 :  NITROSYL COMPLEX OF THE D121I VARIANT OF CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS
 
Authors :  D. D. Gahfoor, D. Kekilli, G. H. Abdullah, F. S. N. Dworkowski, H. G. Hass M. T. Wilson, M. A. Hough, R. W. Strange
Date :  31 Oct 14  (Deposition) - 09 Sep 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Proximal No, Gas Sensing, Nitric Oxide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. D. Ghafoor, D. Kekilli, G. H. Abdullah, F. S. N. Dworkowski, H. G. Hassan, M. T. Wilson, R. W. Strange, M. A. Hough
Hydrogen Bonding Of The Dissociated Histidine Ligand Is Not Required For Formation Of A Proximal No Adduct In Cytochrome C'.
J. Biol. Inorg. Chem. V. 20 949 2015
PubMed-ID: 26100643  |  Reference-DOI: 10.1007/S00775-015-1278-Y

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Synonym: CYTOCHROME C PRIME

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
2NO1Ligand/IonNITRIC OXIDE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1HEC2Ligand/IonHEME C
2NO-1Ligand/IonNITRIC OXIDE
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , LEU A:16 , THR A:17 , MET A:19 , TRP A:56 , PHE A:59 , GLY A:65 , ASP A:67 , ILE A:72 , GLN A:83 , PHE A:86 , CYS A:116 , CYS A:119 , TYR A:123 , ARG A:124 , NO A:129 , HOH A:2039 , HOH A:2057 , HOH A:2176 , HOH A:2177BINDING SITE FOR RESIDUE HEC A 128
2AC2SOFTWAREHIS A:120 , ARG A:124 , HEC A:128BINDING SITE FOR RESIDUE NO A 129

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D4X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D4X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D4X)

(-) Exons   (0, 0)

(no "Exon" information available for 4D4X)

(-) 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:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4d4x A   1 xFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHIAYRKK 126
                            |       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  (0, 0)

(no "SCOP Domain" information available for 4D4X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D4X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D4X)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 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 ]
    NO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4d4x)
 
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
  4d4x
    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 2xm0 2xm4 2ykz 2yl0 2yl1 2yl3 2yl7 2yld 2ylg 2yli 3zqv 3zqy 3ztm 3ztz 3zwi 4cda 4cdv 4cdy 4cip 4cjg 4cjo 4d4n 4wgy 4wgz 5agf 5jli 5jp7 5jra 5js5 5jsl 5jt4 5jua 5jve

(-) Related Entries Specified in the PDB File

4d4n NITROSYL COMPLEX OF THE D121A VARIANT OF CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS