Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  PUTATIVE ACETYLTRANSFERASE FROM AGROBACTERIUM TUMEFACIENS STR. C58
 
Authors :  T. A. Binkowski, X. Xu, A. Edwards, A. Savchenko, A. Joachimiak, Midwes For Structural Genomics (Mcsg)
Date :  30 Aug 06  (Deposition) - 27 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acetyltransferase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Binkowski, X. Xu, A. Edwards, A. Savchenko, A. Joachimiak
Putative Acetyltransferase From Agrobacterium Tumefaciens Str. C58
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACETYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ATU2231
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58
    Synonym: AGR_C_4057P

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO48Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:89 , GLY A:95 , ARG A:96 , GLY A:97 , TYR A:98 , GLY A:99 , ARG A:100 , PHE A:132 , HOH A:7290 , HOH B:8297BINDING SITE FOR RESIDUE PO4 A 1285
2AC2SOFTWAREPO4 A:7285 , GLY B:95 , ARG B:96 , GLY B:97 , TYR B:98 , GLY B:99 , ARG B:100 , PHE B:132 , HOH B:8294BINDING SITE FOR RESIDUE PO4 B 2285
3AC3SOFTWAREARG A:148 , HOH A:7311 , ARG B:76 , TYR B:116 , LYS B:117 , LYS B:142 , HOH B:8309 , HOH B:8411BINDING SITE FOR RESIDUE PO4 B 3285
4AC4SOFTWAREARG A:76 , TYR A:116 , LYS A:117 , ARG B:148BINDING SITE FOR RESIDUE PO4 A 4285
5AC5SOFTWAREASN A:27 , PRO A:28 , SER A:29 , HOH A:7413 , ARG B:76BINDING SITE FOR RESIDUE PO4 A 5285
6AC6SOFTWAREARG A:76 , ASN B:27 , PRO B:28 , SER B:29BINDING SITE FOR RESIDUE PO4 B 6285
7AC7SOFTWAREARG A:96 , TYR A:98 , THR A:101 , GLY B:95 , ARG B:100 , PO4 B:2285BINDING SITE FOR RESIDUE PO4 A 7285
8AC8SOFTWAREILE B:84 , GLU B:85 , ASN B:86 , VAL B:87 , LEU B:121 , THR B:122 , TYR B:133 , HOH B:8293BINDING SITE FOR RESIDUE PO4 B 8285

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DXQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr B:35 -Gln B:36
2Gln B:36 -Glu B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DXQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DXQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2DXQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:147
 aligned with A9CI53_AGRFC | A9CI53 from UniProtKB/TrEMBL  Length:150

    Alignment length:147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       
         A9CI53_AGRFC     4 DAISLRAAGPGDLPGLLELYQVLNPSDPELTTQEAGAVFAAMLAQPGLTIFVATENGKPVATATLLIVPNLTRAARPYAFIENVVTLEARRGRGYGRTVVRHAIETAFGANCYKVMLLTGRHDPAVHAFYESCGFVQNKTGFQIRQD 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dxqA00 A:4-150  [code=3.40.630.30, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee..hhhhhh.eeeeeeee.hhhhh..hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dxq A   4 DAISLRAAGPGDLPGLLELYQVLNPSDPELTTQEAGAVFAAmLAQPGLTIFVATENGKPVATATLLIVPNLTRAARPYAFIENVVTLEARRGRGYGRTVVRHAIETAFGANCYKVmLLTGRHDPAVHAFYESCGFVQNKTGFQIRQD 150
                                    13        23        33        43 |      53        63        73        83        93       103       113     | 123       133       143       
                                                                    45-MSE                                                                   119-MSE                           


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with A9CI53_AGRFC | A9CI53 from UniProtKB/TrEMBL  Length:150

    Alignment length:144
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145    
         A9CI53_AGRFC     6 ISLRAAGPGDLPGLLELYQVLNPSDPELTTQEAGAVFAAMLAQPGLTIFVATENGKPVATATLLIVPNLTRAARPYAFIENVVTLEARRGRGYGRTVVRHAIETAFGANCYKVMLLTGRHDPAVHAFYESCGFVQNKTGFQIRQ 149
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2dxqB00 B:6-149  [code=3.40.630.30, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhh..........hhhhhhhhhhh..eeeeeeee..eeeeeeeeeee..hhhhhh.eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dxq B   6 ISLRAAGPGDLPGLLELYQVLNPSDPELTTQEAGAVFAAmLAQPGLTIFVATENGKPVATATLLIVPNLTRAARPYAFIENVVTLEARRGRGYGRTVVRHAIETAFGANCYKVmLLTGRHDPAVHAFYESCGFVQNKTGFQIRQ 149
                                    15        25        35        45        55        65        75        85        95       105       115   |   125       135       145    
                                                                  45-MSE                                                                   119-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 2DXQ)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DXQ)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A9CI53_AGRFC | A9CI53)
molecular function
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln B:36 - Glu B:37   [ RasMol ]  
    Thr B:35 - Gln B:36   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  2dxq
    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
  A9CI53_AGRFC | A9CI53
    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
  A9CI53_AGRFC | A9CI53
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2DXQ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DXQ)