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 D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM ALCALIGENES FAECALIS COMPLEXED WITH NAD+ AND AN INHIBITOR MALONATE
 
Authors :  H. Kanazawa, M. Tsunoda, M. M. Hoque, K. Suzuki, T. Yamamoto, A. Takenak
Date :  19 Apr 16  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Short-Chain Dehydrogenases/Reductases, Inhibitor, Complex, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kanazawa, M. M. Hoque, M. Tsunoda, K. Suzuki, T. Yamamoto, G. Kawai, J. Kondo, A. Takenaka
Structural Insights Into The Catalytic Reaction Trigger And Inhibition Of D-3-Hydroxybutyrate Dehydrogenase
Acta Crystallogr. , Sect. F V. 72 507 2016
PubMed-ID: 27380367  |  Reference-DOI: 10.1107/S2053230X16007767

(-) Compounds

Molecule 1 - 3-HYDROXYBUTYRATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UZ73_03715
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Synonym: D-3-HYDROXYBUTYRATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MLA1Ligand/IonMALONIC ACID
3NA1Ligand/IonSODIUM ION
4NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MLA4Ligand/IonMALONIC ACID
3NA-1Ligand/IonSODIUM ION
4NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , THR A:13 , SER A:14 , GLY A:15 , ILE A:16 , ASN A:34 , PHE A:36 , ALA A:62 , ASP A:63 , LEU A:64 , ASN A:90 , GLY A:92 , LEU A:113 , ILE A:140 , ALA A:141 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , TRP A:187 , VAL A:188 , THR A:190 , PRO A:191 , LEU A:192 , VAL A:193 , MLA A:302 , HOH A:436 , HOH A:444 , HOH A:487 , HOH A:539 , HOH A:583 , HOH A:606binding site for residue NAD A 301
2AC2SOFTWAREGLN A:94 , SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , LEU A:192 , GLN A:196 , NAD A:301 , HOH A:403binding site for residue MLA A 302
3AC3SOFTWAREARG A:260 , HOH A:426 , HOH A:468binding site for residue NA A 303
4AC4SOFTWARESER A:149 , VAL A:150 , LYS A:219 , HOH A:594binding site for residue CL A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B4U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B4U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B4U)

(-) Exons   (0, 0)

(no "Exon" information available for 5B4U)

(-) 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
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b4u A   1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 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  (0, 0)

(no "SCOP Domain" information available for 5B4U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B4U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B4U)

(-) Gene Ontology  (4, 4)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAD  [ 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 5b4u)
 
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
  5b4u
    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
  D0VWQ0_ALCFA | D0VWQ0
    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)
  1.1.1.30
    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
  D0VWQ0_ALCFA | D0VWQ0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D0VWQ0_ALCFA | D0VWQ0: 2yz7 3vdq 3vdr 3w8d 3w8e 3w8f 5b4t 5b4v

(-) Related Entries Specified in the PDB File

5b4t 5b4v