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 ENOYL-ACP REDUCTASES I (FABI) FROM B. SUBTILIS (COMPLEX WITH NAD AND INH)
 
Authors :  K. -H. Kim, B. H. Ha, S. J. Kim, S. K. Hong, K. Y. Hwang, E. E. Kim
Date :  19 Aug 10  (Deposition) - 05 Jan 11  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Fatty Acid Synthesis, Rossmann-Like Fold, Enoyl-Acp Reductases, Nadh Binding, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. -H. Kim, B. H. Ha, S. J. Kim, S. K. Hong, K. Y. Hwang, E. E. Kim
Crystal Structures Of Enoyl-Acp Reductases I (Fabi) And Iii (Fabl) From B. Subtilis
J. Mol. Biol. V. 406 403 2011
PubMed-ID: 21185310  |  Reference-DOI: 10.1016/J.JMB.2010.12.003

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
    Chains: A
    EC Number: 1.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FABI
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168
    Synonym: ENOYL-ACP REDUCTASES I, FABI, NADH-DEPENDENT ENOYL-ACP REDUCTASE, COLD SHOCK-INDUCED PROTEIN 15, CSI15, VEGETATIVE PROTEIN 241, VEG241

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1IMJ1Ligand/Ion(2E)-N-[(1,2-DIMETHYL-1H-INDOL-3-YL)METHYL]-N-METHYL-3-(7-OXO-5,6,7,8-TETRAHYDRO-1,8-NAPHTHYRIDIN-3-YL)PROP-2-ENAMIDE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1IMJ4Ligand/Ion(2E)-N-[(1,2-DIMETHYL-1H-INDOL-3-YL)METHYL]-N-METHYL-3-(7-OXO-5,6,7,8-TETRAHYDRO-1,8-NAPHTHYRIDIN-3-YL)PROP-2-ENAMIDE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , VAL A:15 , ALA A:16 , SER A:20 , ILE A:21 , ALA A:41 , CYS A:66 , ASP A:67 , VAL A:68 , THR A:69 , CYS A:94 , ILE A:95 , ALA A:96 , LEU A:146 , THR A:147 , LYS A:165 , ALA A:191 , GLY A:192 , PRO A:193 , ILE A:194 , THR A:196 , LEU A:197 , SER A:198 , HOH A:271 , HOH A:274 , HOH A:276 , HOH A:282 , IMJ A:301 , HOH A:487 , HOH A:500 , HOH A:501BINDING SITE FOR RESIDUE NAD A 1501
2AC2SOFTWAREPHE A:97 , ALA A:98 , TYR A:148 , ASN A:157 , TYR A:158 , SER A:198 , ILE A:202 , HOH A:299 , HOH A:384 , NAD A:1501BINDING SITE FOR RESIDUE IMJ A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OIG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OIG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OIG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OIG)

(-) Exons   (0, 0)

(no "Exon" information available for 3OIG)

(-) 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:260
 aligned with FABI_BACSU | P54616 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:260
                                                                                                                                                                                                                                                                                           258  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       | -
           FABI_BACSU     1 MNFSLEGRNIVVMGVANKRSIAWGIARSLHEAGARLIFTYAGERLEKSVHELAGTLDRNDSIILPCDVTNDAEIETCFASIKEQVGVIHGIAHCIAFANKEELVGEYLNTNRDGFLLAHNISSYSLTAVVKAARPMMTEGGSIVTLTYLGGELVMPNYNVMGVAKASLDASVKYLAADLGKENIRVNSISAGPIRTLSAKGISDFNSILKDIEERAPLRRTTTPEEVGDTAAFLFSDMSRGITGENLHVDSGFHITAR--   -
               SCOP domains d3oiga_ A: Enoyl-ACP reductase                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------adh_short_C2-3oigA01 A:14-254                                                                                                                                                                                                                    ------ Pfam domains
         Sec.struct. author ........eeeee......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh...eeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oig A   1 MNFSLEGRNIVVMGVANKRSIAWGIARSLHEAGARLIFTYAGERLEKSVHELAGTLDRNDSIILPCDVTNDAEIETCFASIKEQVGVIHGIAHCIAFANKEELVGEYLNTNRDGFLLAHNISSYSLTAVVKAARPMMTEGGSIVTLTYLGGELVMPNYNVMGVAKASLDASVKYLAADLGKENIRVNSISAGPIRTLSAKGISDFNSILKDIEERAPLRRTTTPEEVGDTAAFLFSDMSRGITGENLHVDSGFHITARLE 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OIG)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (FABI_BACSU | P54616)
molecular function
    GO:0004318    enoyl-[acyl-carrier-protein] reductase (NADH) activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + NAD+ = trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0070417    cellular response to cold    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0030497    fatty acid elongation    The elongation of a fatty acid chain by the sequential addition of two-carbon units.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

 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
    IMJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3oig)
 
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
  3oig
    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
  FABI_BACSU | P54616
    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)
  1.3.1.9
    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
  FABI_BACSU | P54616
    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
        FABI_BACSU | P54616: 3oif

(-) Related Entries Specified in the PDB File

3oic ENOYL-ACP REDUCTASES III, APO-FORM
3oid ENOYL-ACP REDUCTASES III IN COMPLEX WITH NAD AND TRICLOSAN
3oif ENOYL-ACP REDUCTASES I IN COMPLEX WITH NAD AND TRICLOSAN