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 A88G MUTANT, IN COMPLEX WITH AMPPNP AND PROPIONATE
 
Authors :  A. M. Murthy, S. Mathivanan, S. Chittori, H. S. Savithri, M. R. N. Murthy
Date :  04 Jan 15  (Deposition) - 23 Sep 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Kinase, Tdcd Mutant, Amppnp, Propionate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. V. Murthy, S. Mathivanan, S. Chittori, H. S. Savithri, M. R. N. Murthy
Structures Of Substrate- And Nucleotide-Bound Propionate Kinase From Salmonella Typhimurium: Substrate Specificity And Phosphate-Transfer Mechanism
Acta Crystallogr. , Sect. D V. 71 1640 2015
PubMed-ID: 26249345  |  Reference-DOI: 10.1107/S1399004715009992

(-) Compounds

Molecule 1 - PROPIONATE KINASE
    Chains: A
    EC Number: 2.7.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSET C PRSET C PRSETPRSET PRSET C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 4-397
    Gene: TDCD, OXD-2, STM3242
    Mutation: YES
    Organism Scientific: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / ATCC 700720)
    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  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2GOL1Ligand/IonGLYCEROL
3PPI1Ligand/IonPROPANOIC ACID
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2GOL2Ligand/IonGLYCEROL
3PPI2Ligand/IonPROPANOIC ACID
4SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:180 , ARG A:184binding site for residue SO4 A 401
2AC2SOFTWAREARG A:306 , HIS A:307 , HOH A:549binding site for residue GOL A 402
3AC3SOFTWAREHIS A:175 , HIS A:203 , GLY A:205 , ASN A:206 , GLY A:207 , ASP A:278 , LEU A:279 , ARG A:280 , GLU A:283 , GLY A:325 , GLY A:326 , ILE A:327 , ASN A:330 , PPI A:404 , HOH A:559binding site for residue ANP A 403
4AC4SOFTWAREHIS A:175 , GLY A:207 , MET A:223 , ARG A:236 , ANP A:403 , HOH A:526binding site for residue PPI A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XH5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XH5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XH5)

(-) Exons   (0, 0)

(no "Exon" information available for 4XH5)

(-) 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee.....eeeeeeee......ee......ee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee..........ee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhh.......eeeeeee...eeeeeee..eeeee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee........eeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xh5 A   4 FPVVLVINCGSSSIKFSVLDVATCDVLMAGIADGMTENAFLSINDKPINLAHSNYEDALKAIAFELEKRDLTDSVALIGHRIGHGGELFTQSVIITDEIIDNIRRVSPLAPLHNYANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLGVRRYGFHGTSHRYVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDVDFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERARLAIKTFVHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLGVLGLTLDVEMNKQPNSHGERIISANPSQVICAVIPTNEEKMIALDAIHLGNVKA 397
                                    13        23        33    ||  44   ||   55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395  
                                                             38|      48|                                                                                                                                                                                                                                                                                                                                                           
                                                              40       50
   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 4XH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XH5)

(-) 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
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PPI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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
(no "Cis Peptide Bonds" information available for 4xh5)
 
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
  4xh5
    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 4fwq 4fwr 4fws 4xh1 4xh4

(-) Related Entries Specified in the PDB File

4xh1 4xh4