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 SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH GTP
 
Authors :  S. Chittori, H. S. Savithri, M. R. N. Murthy
Date :  01 Jul 12  (Deposition) - 19 Jun 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Kinase, Acetate And Sugar Kinases/Hsc70/Actin (Askha) Superfamily, Tdcd, Gtp, Short-Chain Fatty Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chittori, D. K. Simanshu, S. Banerjee, A. M. V. Murthy, S. Mathivanan, H. S. Savithri, M. R. N. Murthy
Mechanistic Features Of Salmonella Typhimurium Propionate Kinase (Tdcd): Insights From Kinetic And Crystallographic Studies.
Biochim. Biophys. Acta V. 1834 2036 2013
PubMed-ID: 23747922  |  Reference-DOI: 10.1016/J.BBAPAP.2013.05.020

(-) Compounds

Molecule 1 - PROPIONATE KINASE
    Chains: A
    EC Number: 2.7.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OXD-2, STM3242, TDCD
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:175 , GLY A:207 , ARG A:236 , GTP A:503BINDING SITE FOR RESIDUE EDO A 501
2AC2SOFTWAREHIS A:316 , GLY A:343 , VAL A:344BINDING SITE FOR RESIDUE EDO A 502
3AC3SOFTWAREHIS A:175 , HIS A:203 , ASN A:206 , GLY A:207 , ASP A:278 , LEU A:279 , ARG A:280 , GLU A:283 , GLY A:326 , ILE A:327 , ASN A:330 , EDO A:501 , HOH A:660BINDING SITE FOR RESIDUE GTP A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FWQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FWQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FWQ)

(-) 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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4fwqa1 A:4-192 Propionate kinase                                                                                                                                                            d4fwqa2 A:193-397 Propionate kinase                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee.....eeeeeeee.....eeeeee.....eeee..hhhhhhhhhhhhhhhh.hhh.eeeeeeee..........ee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhh..hhhh.eeeeeee...eeeeeee..eeeee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee........eeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fwq A   4 FPVVLVINCGSSSIKFSVLDVATCDVLMAGIADGMNTENAFLSINGDKPINLAHSNYEDALKAIAFELEKRDLTDSVALIGHRIAHGGELFTQSVIITDEIIDNIRRVSPLAPLHNYANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLGVRRYGFHGTSHRYVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDVDFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERARLAIKTFVHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLGVLGLTLDVEMNKQPNSHGERIISANPSQVICAVIPTNEEKMIALDAIHLGNVKA 397
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ 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 4fwq)
 
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
  4fwq
    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
  TDCD_SALTY | O06961
    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)
  2.7.2.15
    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
  TDCD_SALTY | O06961
    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
        TDCD_SALTY | O06961: 1x3m 1x3n 2e1y 2e1z 2e20 4fwk 4fwl 4fwm 4fwn 4fwo 4fwp 4fwr 4fws 4xh1 4xh4 4xh5

(-) Related Entries Specified in the PDB File

1x3m CRYSTAL STRUCTURE OF ADP BOUND PROPIONATE KINASE (TDCD) FROM SALMONELLA TYPHIMURIUM
1x3n CRYSTAL STRUCTURE OF AMPPNP BOUND PROPIONATE KINASE (TDCD) FROM SALMONELLA TYPHIMURIUM
2e1y CRYSTAL STRUCTURE OF PROPIONATE KINASE (TDCD) FROM SALMONELLA TYPHIMURIUM
2e1z CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH DIADENOSINE TETRAPHOSPHATE (AP4A) OBTAINED AFTER CO-CRYSTALLIZATION WITH ATP
2e20 CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH DIADENOSINE TETRAPHOSPHATE (AP4A)
4fwk
4fwl
4fwm
4fwn
4fwo
4fwp
4fwr
4fws