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 :  CRYSTAL STRUCTURE OF THE ZN-DIRECTED TETRAMER OF THE ENGINEERED CYT CB562 VARIANT, A104/57G AB3
 
Authors :  F. A. Tezcan, W. J. Song
Date :  06 Aug 14  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Designed Enzyme, Zn-Coordinating Protein, Tetramer Assembly, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. J. Song, A. F. Tezcan
A Designed Supramolecular Protein Assembly With In Vivo Enzymatic Activity
Science V. 346 1525 2014
PubMed-ID: 25525249  |  Reference-DOI: 10.1126/SCIENCE.1259680

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-128
    Gene: CYBC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOCHROME B-562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:4 , MET A:7 , PHE A:61 , CYS A:98 , CYS A:101 , HIS A:102 , CA A:204binding site for residue HEM A 201
2AC2SOFTWAREASP A:5 , GLU A:8 , CA A:206binding site for residue CA A 202
3AC3SOFTWARELYS A:19 , ASP A:21 , HOH A:319binding site for residue CA A 203
4AC4SOFTWAREGLU A:4 , ASP A:5 , GLU A:8 , HEM A:201 , HOH A:301 , HOH A:316 , HOH A:321binding site for residue CA A 204
5AC5SOFTWAREGLU A:8 , CA A:202 , HOH A:311binding site for residue CA A 206
6AC6SOFTWAREHIS A:63 , HIS A:73 , HIS A:77 , HOH A:315binding site for residue ZN A 207
7AC7SOFTWAREGLU A:86 , HIS A:89 , HIS A:100 , HOH A:318binding site for residue ZN A 208

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:96 -A:96

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His A:59 -Asp A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U9E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U9E)

(-) Exons   (0, 0)

(no "Exon" information available for 4U9E)

(-) 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:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4u9e A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSMHDFRHGFWILIGQIHDALHLANEGKVKEAQHAAEQLKCTCNHCHQAYR 106
                                    10        20        30        40 ||     65        75        85        95       105 
                                                                    42|                                                
                                                                     58
   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 4U9E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U9E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U9E)

(-) 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:59 - Asp A:60   [ RasMol ]  
 
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
  4u9e
    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
  C562_ECOLX | P0ABE7
    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
  C562_ECOLX | P0ABE7
    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
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi

(-) Related Entries Specified in the PDB File

4u9d