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 C143S XANTHOMONAS CAMPESTRIS OLEA BOUND WITH MYRISTIC ACID AND MYRISOTOYL-COA
 
Authors :  B. R. Goblirsch
Date :  21 May 13  (Deposition) - 23 Jul 14  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thiolase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Goblirsch, M. R. Jensen, F. A. Mohamed, L. P. Wackett, C. M. Wilmot
Substrate Trapping In Crystals Of The Thiolase Olea Identifies Three Channels That Enable Long Chain Olefin Biosynthesis.
J. Biol. Chem. V. 291 26698 2016
PubMed-ID: 27815501  |  Reference-DOI: 10.1074/JBC.M116.760892

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACP] SYNTHASE III
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FABH, XCC0212
    Mutation: YES
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 190485
    Strain: ATCC 33913 / NCPPB 528 / LMG 568

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MYA1Ligand/IonTETRADECANOYL-COA
2MYR1Ligand/IonMYRISTIC ACID
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:198 , ALA A:199 , THR A:248 , THR A:250 , VAL A:287 , SER A:288 , HIS A:291 , HOH A:616 , HOH A:633 , HOH A:676 , HOH A:738BINDING SITE FOR RESIDUE PEG A 401
2AC2SOFTWAREASP A:35 , ARG A:73 , ILE A:309 , GLU A:312 , HIS A:313 , HOH A:658 , HOH A:705 , HOH A:717BINDING SITE FOR RESIDUE PEG A 402
3AC3SOFTWARESER B:143 , LEU B:253 , GLY B:257 , ILE B:258 , ILE B:284 , HIS B:285 , HIS B:291 , ASN B:315 , LEU B:343 , ILE B:345 , GLY B:346 , SER B:347 , MYA B:402BINDING SITE FOR RESIDUE MYR B 401
4AC4SOFTWARETHR B:60 , VAL B:66 , ALA B:67 , SER B:112 , GLU B:171 , THR B:172 , PHE B:194 , ARG B:195 , LEU B:198 , ALA B:199 , THR B:202 , CYS B:239 , ASN B:242 , THR B:250 , ARG B:251 , LEU B:253 , VAL B:287 , SER B:288 , PRO B:290 , GLY B:317 , MYR B:401 , HOH B:511 , HOH B:524 , HOH B:662BINDING SITE FOR RESIDUE MYA B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KU3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:117 -Pro A:118
2Gly A:348 -Leu A:349
3Glu B:117 -Pro B:118
4Gly B:348 -Leu B:349

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KU3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KU3)

(-) Exons   (0, 0)

(no "Exon" information available for 4KU3)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee..eeeehhhhhhhhhhhhhhhh.............eeee.....hhhhhhhhhhhhhhhhh..hhh.eeeeee..........hhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeeeeeeee.hhh....eeeeeeeee.hhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhh.hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ku3 A  20 HMLFQNVSIAGLAHIDAPHTLTSKEINERLQPTYDRLGIKTDVLGDVAGIHARRLWDQDVQASDAATQAARKALIDANIGIEKIGLLINTSVSRDYLEPSTASIVSGNLGVSDHCMTFDVANASLAFINGMDIAARMLERGEIDYALVVDGETANLVYEKTLERMTSPDVTEEEFRNELAALTLGCGAAAMVMARSELVPDAPRYKGGVTRSATEWNKLCRGNLDRMVTDTRLLLIEGIKLAQKTFVAAKQVLGWAVEELDQFVIHQVSRPHTAAFVKSFGIDPAKVMTIFGEHGNIGPASVPIVLSKLKELGRLKKGDRIALLGIGSGLNCSMAEVVW 358
                                    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       309       319       329       339       349         


Chain B from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeehhhhhhhhhhhhhhhh...hhhhhh....eeee.....hhhhhhhhhhhhhhhhhh.hhh.eeeeee..........hhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eeeeeeeee.hhh....eeeeeeeee.hhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ku3 B  22 LFQNVSIAGLAHIDAPHTLTSKEINERLQPTYDRLGIKTDVLGDVAGIHARRLWDQDVQASDAATQAARKALIDANIGIEKIGLLINTSVSRDYLEPSTASIVSGNLGVSDHCMTFDVANASLAFINGMDIAARMLERGEIDYALVVDGETANLVYEKTLERMTSPDVTEEEFRNELAALTLGCGAAAMVMARSELVPDAPRYKGGVTRSATEWNKLCRGNLDRMVTDTRLLLIEGIKLAQKTFVAAKQVLGWAVEELDQFVIHQVSRPHTAAFVKSFGIDPAKVMTIFGEHGNIGPASVPIVLSKLKELGRLKKGDRIALLGIGSGLNCSMAEVVW 358
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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 4KU3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KU3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KU3)

(-) Gene Ontology  (6, 6)

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
    MYA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MYR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ 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
    Glu A:117 - Pro A:118   [ RasMol ]  
    Glu B:117 - Pro B:118   [ RasMol ]  
    Gly A:348 - Leu A:349   [ RasMol ]  
    Gly B:348 - Leu B:349   [ 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
  4ku3
    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
  Q8PDX2_XANCP | Q8PDX2
    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
  Q8PDX2_XANCP | Q8PDX2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8PDX2_XANCP | Q8PDX2: 3row 3s1z 3s20 3s21 3s23 4kti 4ktm 4ku2 4ku5

(-) Related Entries Specified in the PDB File

3row 3s21 3s23 4kt1 4ku2