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

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE ATP-GRASP SUPERFAMILY PROTEIN FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  R. Sugadev, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  11 Jun 08  (Deposition) - 05 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Protein, Atp-Grasp Superfamily, Archaeoglobus Fulgidus, 10040D, Psi-Ii, Nysgrc. , Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Unknown Function, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sugadev, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Atp-Grasp Superfamily Protein From Archaeoglobus Fulgidus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE ATP-GRASP SUPERFAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BS)
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: AF_1061
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:8 , ILE A:76 , ALA A:77 , PRO A:78BINDING SITE FOR RESIDUE ACT A 1428

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DF7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DF7)

(-) Exons   (0, 0)

(no "Exon" information available for 3DF7)

(-) 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:301
 aligned with O29201_ARCFU | O29201 from UniProtKB/TrEMBL  Length:304

    Alignment length:305
                             1                                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299     
         O29201_ARCFU     - -MKLFLFEFATCGERIEDSTAVEGLAMFKSAFDGFKNYYEITGFVRPEFSCLFTLPVDSMDSMEKYLEKSDAFLIIAPEDDFLLYTLTKKAEKYCENLGSSSRAIAVTSDKWELYKKLRGEVQVPQTSLRPLDCKFIIKPRTACAGEGIGFSDEVPDGHIAQEFIEGINLSVSLAVGEDVKCLSVNEQIINNFRYAGAVVPARISDEVKREVVEEAVRAVECVEGLNGYVGVDIVYSDQPYVIEINARLTTPVVAFSRAYGASVADLLAGGEVKHVRRQMVRKSKSAEKPYVSVGDYTLEIIDLD 304
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhh...hhhhhhhhhhhhhhhhhhhh...eee...hhhhh........hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhh.......ee.......eeeee....----..........eeeee....eeeeeeeee...eeeeeeeeeeee..eeeeeee....hhhhhhhhhhhhhhhhh......eeeeeeeee...eeeeeee...hhhhhhhhhhhh.hhhhhhh.........eeeeeee......eee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3df7 A   1 SLKLFLFEFATCGERIEDSTAVEGLAmFKSAFDGFKNYYEITGFVRPEFSCLFTLPVDSmDSmEKYLEKSDAFLIIAPEDDFLLYTLTKKAEKYCENLGSSSRAIAVTSDKWELYKKLRGEVQVPQTSLRPLDCKFIIKPRTAC----IGFSDEVPDGHIAQEFIEGINLSVSLAVGEDVKCLSVNEQIINNFRYAGAVVPARISDEVKREVVEEAVRAVECVEGLNGYVGVDIVYSDQPYVIEINARLTTPVVAFSRAYGASVADLLAGGEVKHVRRQmVRKSKSAEKPYVSVGDYTLEIIDLD 305
                                    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     
                                                     27-MSE                           60-MSE                                                                             144  149                                                                                                                                280-MSE                     
                                                                                         63-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 3DF7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DF7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DF7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O29201_ARCFU | O29201)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:200 - Pro A:201   [ 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
  3df7
    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
  O29201_ARCFU | O29201
    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
  O29201_ARCFU | O29201
    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 3DF7)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DF7)