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 E. COLI FABI IN COMPLEX WITH NADH AND CG400549
 
Authors :  M. Tareilus, J. Schiebel, A. Chang, S. Shah, P. J. Tonge, C. Kisker
Date :  22 Mar 14  (Deposition) - 16 Apr 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Short-Chain Dehydrogenase/Reductase Superfamily, Fatty Acid Biosynthesis, Lipid Synthesis, Ecfabi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Schiebel, A. Chang, S. Shah, Y. Lu, L. Liu, P. Pan, M. W. Hirschbeck, M. Tareilus, S. Eltschkner, W. Yu, J. E. Cummings, S. E. Knudson, G. R. Bommineni, S. G. Walker, R. A. Slayden, C. A. Sotriffer, P. J. Tonge, C. Kisker
Rational Design Of Broad Spectrum Antibacterial Activity Based On A Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor.
J. Biol. Chem. V. 289 15987 2014
PubMed-ID: 24739388  |  Reference-DOI: 10.1074/JBC.M113.532804

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
    Chains: A, B
    EC Number: 1.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET23B
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Strain: BL21(DE3)
    Synonym: ENOYL-ACP REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2PT62Ligand/Ion1-(3-AMINO-2-METHYLBENZYL)-4-[2-(THIOPHEN-2-YL)ETHOXY]PYRIDIN-2(1H)-ONE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2PT64Ligand/Ion1-(3-AMINO-2-METHYLBENZYL)-4-[2-(THIOPHEN-2-YL)ETHOXY]PYRIDIN-2(1H)-ONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ALA A:15 , SER A:19 , ILE A:20 , GLN A:40 , LEU A:44 , CYS A:63 , ASP A:64 , VAL A:65 , SER A:91 , ILE A:92 , GLY A:93 , ILE A:119 , LEU A:144 , SER A:145 , LYS A:163 , ALA A:189 , GLY A:190 , PRO A:191 , ILE A:192 , PT6 A:1259 , HOH A:2013 , HOH A:2014 , HOH A:2016 , HOH A:2018 , HOH A:2025 , HOH A:2119BINDING SITE FOR RESIDUE NAI A1258
2AC2SOFTWAREGLY B:13 , ALA B:15 , SER B:19 , ILE B:20 , GLN B:40 , CYS B:63 , ASP B:64 , VAL B:65 , SER B:91 , ILE B:92 , GLY B:93 , LEU B:144 , SER B:145 , LYS B:163 , ALA B:189 , PRO B:191 , ILE B:192 , PT6 B:1259 , HOH B:2011 , HOH B:2012 , HOH B:2035 , HOH B:2071BINDING SITE FOR RESIDUE NAI B1258
3AC3SOFTWAREGLY A:93 , PHE A:94 , ALA A:95 , LEU A:100 , TYR A:146 , ILE A:153 , PRO A:154 , TYR A:156 , NAI A:1258BINDING SITE FOR RESIDUE PT6 A1259
4AC4SOFTWAREGLY B:93 , PHE B:94 , ALA B:95 , TYR B:146 , ILE B:153 , PRO B:154 , TYR B:156 , NAI B:1258BINDING SITE FOR RESIDUE PT6 B1259

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CV2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CV2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CV2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CV2)

(-) Exons   (0, 0)

(no "Exon" information available for 4CV2)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh..eeeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cv2 A   2 GFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIAVTPIRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMN 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191||     220       230       240       250       
                                                                                                                                                                                                                        192|                                             
                                                                                                                                                                                                                         212                                             


Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cv2 B   2 GFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIEAVTPIRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMN 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191||     219       229       239       249        
                                                                                                                                                                                                                        192|                                              
                                                                                                                                                                                                                         211
   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 4CV2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CV2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CV2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4CV2)

 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
    NAI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PT6  [ 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 4cv2)
 
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
  4cv2
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4CV2)

(-) Related Entries Specified in the PDB File

4cuz CRYSTAL STRUCTURE OF S. AUREUS FABI IN COMPLEX WITH NADPH AND PT173
4cv0 CRYSTAL STRUCTURE OF S. AUREUS FABI IN COMPLEX WITH NADPH AND CG400549 (SMALL UNIT CELL)
4cv1 CRYSTAL STRUCTURE OF S. AUREUS FABI IN COMPLEX WITH NADPH AND CG400549
4cv3 CRYSTAL STRUCTURE OF E. COLI FABI IN COMPLEX WITH NADH AND PT166