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 BETA-KETOACYL-ACP SYNTHASE III-2 (FABH2) (C113A) FROM VIBRIO CHOLERAE CO-CRYSTALLIZED WITH OCTANOYL-COA
 
Authors :  J. Hou, H. Zheng, D. R. Cooper, M. Grabowski, W. F. Anderson, W. Minor, Ce Structural Genomics Of Infectious Diseases (Csgid)
Date :  28 Feb 17  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fabh, Beta-Ketoacyl-Acyl Carrier Protein Synthase Iii, Transferase, Octanoyl-Coa, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hou, H. Zheng, D. R. Cooper, M. Chruszcz, M. D. Chordia, M. Grabowski W. Minor
Crystal Structure Of Beta-Ketoacyl-Acp Synthase Iii-2 (Fabh2) (C113A) From Vibrio Cholerae Co-Crystallized With Octanoyl-Coa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3 PROTEIN 2
    Atcc: 39315
    Chains: A, B
    EC Number: 2.3.1.180
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FABH2, VC_A0751
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1 (STRAIN ATCC 39315 / EL TOR INABA N16961)
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961
    Synonym: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III PROTEIN 2, BETA-KETOACYL-ACP SYNTHASE III 2,KAS III 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CO82Ligand/IonOCTANOYL-COENZYME A
2NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:244 , ASP A:246 , ASP A:305 , HOH A:609 , HOH A:615 , HOH A:649binding site for residue NA A 401
2AC2SOFTWARETHR A:31 , TRP A:35 , ARG A:39 , ALA A:112 , ALA A:113 , ARG A:152 , ASP A:153 , VAL A:156 , PHE A:158 , LEU A:191 , PHE A:212 , GLY A:216 , LYS A:217 , ILE A:219 , HIS A:251 , ALA A:253 , ASN A:254 , ASN A:281 , SER A:283 , PHE A:311 , GLY A:312 , ALA A:313 , HOH A:511 , ILE B:88binding site for residue CO8 A 402
3AC3SOFTWAREGLU B:244 , ASP B:246 , ASP B:305 , HOH B:613 , HOH B:627 , HOH B:648binding site for residue NA B 401
4AC4SOFTWAREILE A:88 , THR B:31 , TRP B:35 , ARG B:39 , ALA B:113 , LEU B:143 , ARG B:152 , ASP B:153 , VAL B:156 , LEU B:191 , PHE B:212 , GLY B:216 , ILE B:219 , HIS B:251 , ALA B:253 , ASN B:254 , ILE B:257 , ASN B:281 , SER B:283 , PHE B:311 , GLY B:312 , ALA B:313 , HOH B:510 , HOH B:549binding site for residue CO8 B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V0P)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:88 -Pro A:89
2Gly A:314 -Leu A:315
3Ile B:88 -Pro B:89
4Gly B:314 -Leu B:315

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V0P)

(-) Exons   (0, 0)

(no "Exon" information available for 5V0P)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeehhhhhh....hhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee..........hhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhh...hhhhhh...eeeeeeeeeee....eeeeeeeee.hhhh..ee....................eehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhh.hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee....................hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v0p A   3 QCYAEITGWGKCLPPATLSNHDLSTFLDTSDEWIQSRTGIEQRRISHVNTSDLATVAAQHAIACAGVSVEEIDLIIVATCSPDSLIPNIASRVQQNLGIPSAAAFDLNAAATGFLYGLETATRLMQASHYRHALVIGAERLSFYLDWTKRDTAVLFGDGAGAVVLSKTEQKVGLQDAQIGCDAQGRDILAVPKFGTAMDRFDADNGYWAFDFVGKEIFKRAVRGMGAAAQQVLARSGLSTEEIDVVIPHQANIRIIQTLCDLAGIAQDKAFVNIHRYGNTSAATVPIALCEALEQGKIKPHDDLLVAAFGAGLTWGAGHIRWGERITPLGKSDAQLPSCDHTALDLLSKAIEHCKRHQ 360
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352        


Chain B from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeehhhhhh....hhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhh.hhh.eeeeeee..........hhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhh...hhhhhh...eeeeeeeeeee....eeeeeeeee.hhhh..ee....................eehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhh.hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee....................hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v0p B   3 QCYAEITGWGKCLPPATLSNHDLSTFLDTSDEWIQSRTGIEQRRISHVNTSDLATVAAQHAIACAGVSVEEIDLIIVATCSPDSLIPNIASRVQQNLGIPSAAAFDLNAAATGFLYGLETATRLMQASHYRHALVIGAERLSFYLDWTKRDTAVLFGDGAGAVVLSKTEQKVGLQDAQIGCDAQGRDILAVPKFGTAMDRFDADNGYWAFDFVGKEIFKRAVRGMGAAAQQVLARSGLSTEEIDVVIPHQANIRIIQTLCDLAGIAQDKAFVNIHRYGNTSAATVPIALCEALEQGKIKPHDDLLVAAFGAGLTWGAGHIRWGERITPLGKSDAQLPSCDHTALDLLSKAIEHCKRHQ 360
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
   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 5V0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V0P)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CO8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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
    Gly A:314 - Leu A:315   [ RasMol ]  
    Gly B:314 - Leu B:315   [ RasMol ]  
    Ile A:88 - Pro A:89   [ RasMol ]  
    Ile B:88 - Pro B:89   [ 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
  5v0p
    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
  FABH2_VIBCH | Q9KLJ3
    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)
  2.3.1.180
    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
  FABH2_VIBCH | Q9KLJ3
    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
        FABH2_VIBCH | Q9KLJ3: 4wzu 4x0o 4x9k 4x9o 5kp2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5V0P)