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 THE MTB ENOYL COA ISOMERASE (RV0632C) IN COMPLEX WITH HYDROXYBUTYRL COA
 
Authors :  J. B. Bruning, N. Gao, E. D. Hernandez, H. Li, N. Dang, L. W. Hung, J. C. Sac Tb Structural Genomics Consortium (Tbsgc)
Date :  19 Jun 12  (Deposition) - 29 May 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Crotonase Superfamily, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bruning, N. Gao, E. D. Hernandez, H. Li, N. Dang, L. W. Hung, S. Moran, J. C. Sacchettini
Crystal Structure And Mechanism Of The Prokaryotic Enoyl Co Isomerase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENOYL-COA HYDRATASE/ISOMERASE FAMILY PROTEIN
    Chains: A
    EC Number: 4.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP16
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ECHA3, MT0660, RV0632C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: ENOYL-COA HYDRATASE HOMOLOG, PROBABLE ENOYL-COA HYDRATASE ECHA3 (ENOYL HYDRASE) (UNSATURATED ACYL-COA HYDRATASE) (CROTONASE)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
13HC1Ligand/Ion3-HYDROXYBUTANOYL-COENZYME A
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
13HC3Ligand/Ion3-HYDROXYBUTANOYL-COENZYME A
2SO49Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:40 , ARG A:43 , ASN A:199 , GLN A:200 , HIS A:201 , HOH A:508 , HOH A:578BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARESER A:2 , LYS A:22 , VAL A:23 , ARG A:56 , GLY A:60 , PHE A:62 , ASP A:63 , LEU A:64 , LEU A:67 , ASN A:129 , GLU A:130 , ILE A:133 , PRO A:138 , HOH A:401 , HOH A:412 , HOH A:487 , HOH A:562 , HOH A:575 , HOH A:588 , HOH A:610BINDING SITE FOR RESIDUE 3HC A 302
3AC3SOFTWARETHR A:150 , ARG A:151 , HOH A:617BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREARG A:9 , HOH A:556BINDING SITE FOR RESIDUE SO4 A 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FNB)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeee........hhhhhhhhhhhhhhhhhhh..eeeee....eee...hhhhhh..hhhhhhhhhhhhhhhhhhhhh....eeeee..eeehhhhhhhh...eeee.....ee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhh...ee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fnb A   0 SMSDPVSYTRKDSIAVISMDDGKVNALGPAMQQALNAAIDNADRDDVGALVITGNGRVFSGGFDLKILTSGEVQPAIDMLRGGFELAYRLLSYPKPVVMACTGHAIAMGAFLLSCGDHRVAAHAYNIQANEVAIGMTIPYAALEIMKLRLTRSAYQQATGLAKTFFGETALAAGFIDEIALPEVVVSRAEEAAREFAGLNQHAHAATKLRSRADALTAIRAGIDGIAAEFGL 231
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
   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 4FNB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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
    3HC  [ 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 4fnb)
 
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
  4fnb
    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
  P96907_MYCTX | P96907
    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)
  4.2.1.17
    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
  P96907_MYCTX | P96907
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        P96907_MYCTX | P96907: 4fn7 4fn8 4fnd 4hc8

(-) Related Entries Specified in the PDB File

4fn7 APO FORM OF ENZYME
4fn8 ACETOACETYL BOUND FORM OF ENZYME
4fnd RELATED ID: RV0632C RELATED DB: TARGETTRACK