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 :  THE L16F MUTANT OF CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS FORM
 
Authors :  D. Kekilli, R. W. Strange, M. A. Hough
Date :  08 May 16  (Deposition) - 08 Mar 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gas Sensor Cytochrome Nitric Oxide, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kekilli, C. A. Petersen, D. A. Pixton, D. D. Ghafoor, G. H. Abdullah, F. S. N. Dworkowski, M. T. Wilson, D. J. Heyes, S. J. O. Hardman, L. M. Murphy, R. W. Strange, N. S. Scrutton, C. R. Andrew, M. A. Hough
Nitric Oxide Complex Of The L16A Mutant Of Cytochrome C Prime From Alcaligenes Xylosoxidans
Chem Sci 2017
PubMed: search  |  Reference-DOI: 10.1039/C6SC04190F

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS
    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  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2HEC1Ligand/IonHEME C
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1ASC2Ligand/IonASCORBIC ACID
2HEC2Ligand/IonHEME C
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID
4SO46Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , PHE A:16 , THR A:17 , ALA A:20 , TRP A:56 , PHE A:59 , GLY A:65 , ASP A:67 , ILE A:72 , PHE A:79 , GLN A:83 , PHE A:86 , CYS A:116 , CYS A:119 , HIS A:120 , ARG A:124 , ASC A:202 , SO4 A:203 , HOH A:305 , HOH A:326 , HOH A:394 , HOH A:412binding site for residue HEC A 201
2AC2SOFTWAREALA A:20 , PHE A:23 , GLY A:113 , HIS A:120 , HEC A:201 , SO4 A:203 , HOH A:314 , HOH A:317 , HOH A:331 , HOH A:387 , HOH A:411binding site for residue ASC A 202
3AC3SOFTWAREHIS A:120 , ARG A:124 , HEC A:201 , ASC A:202 , HOH A:383 , HOH A:410binding site for residue SO4 A 203
4AC4SOFTWAREARG A:69 , LYS A:125 , LYS A:126binding site for residue SO4 A 204
5AC5SOFTWARELYS A:92 , ASP A:103 , LYS A:104 , HOH A:313 , HOH A:343binding site for residue SO4 A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JSL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JSL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JSL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JSL)

(-) Exons   (0, 0)

(no "Exon" information available for 5JSL)

(-) 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.....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jsl A   1 xFAKPEDAVKYRQSAFTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRKK 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 5JSL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JSL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JSL)

(-) 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
    ASC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5jsl)
 
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
  5jsl
    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 4d4x 4wgy 4wgz 5agf 5jli 5jp7 5jra 5js5 5jt4 5jua 5jve

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JSL)