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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHIMERICAL PROTEIN CAPAB
 
Authors :  V. Olivares-Illana, P. Meyer, S. Morera, S. Nessler
Date :  23 Nov 07  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chimerical Protein, P-Loop Protein, Capsule Biogenesis/Degradation, Exopolysaccharide Synthesis, Membrane, Transmembrane, Virulence, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Olivares-Illana, P. Meyer, E. Bechet, V. Gueguen-Chaignon, D. Soulat, S. Lazereg-Riquier, I. Mijakovic, J. Deutscher, A. J. Cozzone, O. Laprevote, S. Morera, C. Grangeasse, S. Nessler
Structural Basis For The Regulation Mechanism Of The Tyrosine Kinase Capb From Staphylococcus Aureus.
Plos Biol. V. 6 E143 2008
PubMed-ID: 18547145  |  Reference-DOI: 10.1371/JOURNAL.PBIO.0060143
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEMBRANE PROTEIN CAPA1, PROTEIN TYROSINE KINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21
    Expression System Vector Type: PLASMID
    Fragment: FUSION PROTEIN CONSISTS OF UNP RESIDUES 194-222 (A8YPQ6) AND 1-230 (A8YPQ5) OF CAPA1 AND CAPB2
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Synonym: CAPA1, CAPB2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:1056 , HOH A:1347 , HOH A:1351 , HOH A:1381 , HOH A:1418BINDING SITE FOR RESIDUE MG A 296
2AC2SOFTWARESER B:1056 , HOH B:1334 , HOH B:1335 , HOH B:1347 , HOH B:1399BINDING SITE FOR RESIDUE MG B 276
3AC3SOFTWAREGLN A:219 , LYS A:220 , PHE A:221 , GLY A:1052 , ALA A:1053 , GLY A:1054 , LYS A:1055 , SER A:1056 , THR A:1057 , ASN A:1211 , ARG A:1212 , HOH A:1260 , HOH A:1351 , HOH A:1360 , HOH A:1378 , HOH A:1383 , GLN B:1016 , HOH B:1393 , HOH B:1401 , HOH B:1418BINDING SITE FOR RESIDUE ADP A 301
4AC4SOFTWAREGLU A:1015 , GLN A:1016 , HOH A:1416 , HOH A:1437 , GLN B:219 , LYS B:220 , PHE B:221 , GLY B:1052 , ALA B:1053 , GLY B:1054 , LYS B:1055 , SER B:1056 , THR B:1057 , ASN B:1211 , ARG B:1212 , HOH B:1236 , HOH B:1333 , HOH B:1340 , HOH B:1347 , HOH B:1355 , HOH B:1392BINDING SITE FOR RESIDUE ADP B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp B:197 -Lys B:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BFV)

(-) 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:241
 aligned with A8YPQ5_STAAU | A8YPQ5 from UniProtKB/TrEMBL  Length:230

    Alignment length:241
                                                      1                                                                                                                                                                                                                      
                                     -         -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
        A8YPQ5_STAAU      - --------------------------MTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPK  215
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeee.............hhhhhh..hhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh......hhhhhhh...hhhhheee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhheeeeeee....hhhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bfv A  197 DKRIKDEEDVEKELGLPVLGSIQKFNMTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPK 1215
                                   206       216     |1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214 
                                                   222|                                                                                                                                                                                                                      
                                                   1001                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with A8YPQ5_STAAU | A8YPQ5 from UniProtKB/TrEMBL  Length:230

    Alignment length:241
                                                      1                                                                                                                                                                                                                      
                                     -         -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
        A8YPQ5_STAAU      - --------------------------MTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPK  215
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh...eeeeee.............hhhhhh..hhhhhhhhhhhhhhhhh.......eeeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhh......hhhhhhh...hhhhheee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhheeeeeee....hhhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bfv B  197 DKRIKDEEDVEKELGLPVLGSIQKFNMTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPK 1215
                                   206       216     |1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214 
                                                   222|                                                                                                                                                                                                                      
                                                   1001
   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 3BFV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A8YPQ5_STAAU | A8YPQ5)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0045226    extracellular polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp B:197 - Lys B:198   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  3bfv
    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
  A8YPQ5_STAAU | A8YPQ5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  A8YPQ6_STAAU | A8YPQ6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  CAP8A_STAAU | P72367
    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
  A8YPQ5_STAAU | A8YPQ5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  A8YPQ6_STAAU | A8YPQ6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CAP8A_STAAU | P72367
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A8YPQ5_STAAU | A8YPQ5: 2ved 4jmp
        A8YPQ6_STAAU | A8YPQ6: 2ved 4jlv

(-) Related Entries Specified in the PDB File

2ved A MUTANT OF THIS PROTEIN