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 CAPSULAR POLYSACCHARIDE ASSEMBLING PROTEIN CAPF FROM STAPHYLOCOCCUS AUREUS
 
Authors :  T. Miyafusa, Y. Tanaka, M. Kuroda, M. Yao, M. Watanabe, T. Ohta, I. Tanak J. M. M. Caaveiro, K. Tsumoto
Date :  09 Jul 11  (Deposition) - 15 Feb 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Cupid Domain, Short-Chain Dehydrogenase/Reductase, Nadph, Udp-4-Hexulose Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Miyafusa, J. M. Caaveiro, Y. Tanaka, K. Tsumoto
Crystal Structure Of The Enzyme Capf Of Staphylococcus Aureus Reveals A Unique Architecture Composed Of Two Functional Domains.
Biochem. J. V. 443 671 2012
PubMed-ID: 22320426  |  Reference-DOI: 10.1042/BJ20112049
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAPSULAR POLYSACCHARIDE SYNTHESIS ENZYME CAP5F
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CAPF, SAV0154
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: MU50 / ATCC 700699

 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, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE5Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:288 , HIS A:290 , GLU A:295 , HIS A:337BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREPHE A:215 , LYS A:216 , SER A:218 , ARG A:219 , TYR A:236 , LYS A:296 , ASP A:330BINDING SITE FOR RESIDUE GOL A 370
3AC3SOFTWARETHR A:246 , GLU A:318 , HOH A:395 , HOH A:411BINDING SITE FOR RESIDUE GOL A 371

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ST7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ST7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ST7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ST7)

(-) Exons   (0, 0)

(no "Exon" information available for 3ST7)

(-) 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:369
 aligned with A0A0H3JP37_S | A0A0H3JP37 from UniProtKB/TrEMBL  Length:369

    Alignment length:369
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360         
         A0A0H3JP37_S     1 MNIVITGAKGFVGKNLKADLTSTTDHHIFEVHRQTKEEELESALLKADFIVHLAGVNRPEHDKEFSLGNVSYLDHVLDILTRNTKKPAILLSSSIQATQDNPYGESKLQGEQLLREYAEEYGNTVYIYRWPNLFGKWCKPNYNSVIATFCYKIARNEEIQVNDRNVELTLNYVDDIVAEIKRAIEGTPTIENGVPTVPNVFKVTLGEIVDLLYKFKQSRLDRTLPKLDNLFEKDLYSTYLSYLPSTDFSYPLLMNVDDRGSFTEFIKTPDRGQVSVNISKPGITKGNHWHHTKNEKFLVVSGKGVIRFRHVNDDEIIEYYVSGDKLEVVDIPVGYTHNIENLGDTDMVTIMWVNEMFDPNQPDTYFLEV 369
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh.eeee..................hhhhhhhhhhh......eeeeeee.hhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.........hhhhhhhhhhhh...........eeeeeehhhhhhhhhhhhhh...ee..ee.....eeeehhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...........eeee..eeeeeeee.....eeeeeee....eeeeee.....eeeeeee.eeeeeeee......eeeeee.....eeee...eeeeeee.....eeeeeee...........ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3st7 A   1 mNIVITGAKGFVGKNLKADLTSTTDHHIFEVHRQTKEEELESALLKADFIVHLAGVNRPEHDKEFSLGNVSYLDHVLDILTRNTKKPAILLSSSIQATQDNPYGESKLQGEQLLREYAEEYGNTVYIYRWPNLFGKWCKPNYNSVIATFCYKIARNEEIQVNDRNVELTLNYVDDIVAEIKRAIEGTPTIENGVPTVPNVFKVTLGEIVDLLYKFKQSRLDRTLPKLDNLFEKDLYSTYLSYLPSTDFSYPLLmNVDDRGSFTEFIKTPDRGQVSVNISKPGITKGNHWHHTKNEKFLVVSGKGVIRFRHVNDDEIIEYYVSGDKLEVVDIPVGYTHNIENLGDTDmVTImWVNEmFDPNQPDTYFLEV 369
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   |   260       270       280       290       300       310       320       330       340      |350|    | 360         
                            |                                                                                                                                                                                                                                                          254-MSE                                                                                      347-MSE    |             
                            1-MSE                                                                                                                                                                                                                                                                                                                                                       351-MSE|             
                                                                                                                                                                                                                                                                                                                                                                                             356-MSE
   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 3ST7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ST7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ST7)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ST7)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3st7)
 
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
  3st7
    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
  A0A0H3JP37_S | A0A0H3JP37
    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
  A0A0H3JP37_S | A0A0H3JP37
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A0A0H3JP37_S | A0A0H3JP37: 2zkl 3vhr 4yrd

(-) Related Entries Specified in the PDB File

2zkl