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 :  THE X-RAY STRUCTURE OF 7BETA-HYDROXYSTEROID DEHYDROGENASE
 
Authors :  F. Wang, R. Wang, Z. Lv, Q. Chen, X. Huo
Date :  19 Aug 16  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Short Chain Dehydrogenase, Steroid Substrates, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wang, J. Wu, D. K. Jin, Y. Chen, Z. Lv, Q. Chen, Q. Miao, X. Huo, F. Wang
Structure Of Nadp(+)-Bound 7 Beta-Hydroxysteroid Dehydrogenase Reveals Two Cofactor-Binding Modes
Acta Crystallogr F Struct V. 73 246 2017 Biol Commun
PubMed-ID: 28471355  |  Reference-DOI: 10.1107/S2053230X17004460

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
    Atcc: 25986
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: COLAER_02088
    Organism Scientific: COLLINSELLA AEROFACIENS ATCC 25986
    Organism Taxid: 411903
    Strain: ATCC 25986

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , THR A:17 , GLU A:18 , GLY A:19 , VAL A:20 , GLY A:21 , GLY A:39 , ARG A:40 , ARG A:41 , ALA A:65 , ASP A:66 , PHE A:67 , VAL A:91 , ALA A:92 , PRO A:192 , HOH A:408 , HOH A:431 , HOH A:472 , HOH A:480 , HOH A:484 , SER B:240 , ASP B:243 , TRP B:244 , HIS B:248 , TYR B:256 , HOH B:405binding site for residue NAP A 301
2AC2SOFTWAREGLY B:15 , THR B:17 , GLU B:18 , GLY B:19 , VAL B:20 , ARG B:40 , ARG B:41 , ALA B:65 , ASP B:66 , PHE B:67 , SER B:68 , VAL B:91 , ALA B:92 , CYS B:93 , VAL B:141 , SER B:143 , TYR B:156 , LYS B:160 , LEU B:186 , GLY B:187 , THR B:188 , THR B:189 , THR B:191 , SER B:193 , HOH B:408 , HOH B:414 , HOH B:444 , HOH B:446 , HOH B:450 , HOH B:464binding site for residue NAP B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GT9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:201 -Pro A:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GT9)

(-) Exons   (0, 0)

(no "Exon" information available for 5GT9)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh.....hhhhhhhh...hhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gt9 A   1 MNLREKYGEWGLILGATEGVGKAFCEKIAAGGMNVVMVGRREEKLNVLAGEIRETYGVETKVVRADFSQPGAAETVFAATEGLDMGFMSYVACLHSFGKIQDTPWEKHEAMINVNVVTFLKCFHHYMRIFAAQDRGAVINVSSMTGISSSPWNGQYGAGKAFILKMTEAVACECEGTGVDVEVITLGTTLTPSLLSNLPGGPQGEAVMKIALTPEECVDEAFEKLGKELSVIAGQRNKDSVHDWKANHTEDEYIRYMGSFYR 262
                                    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  


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhh....hhhhhhhhh...hhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gt9 B   1 MNLREKYGEWGLILGATEGVGKAFCEKIAAGGMNVVMVGRREEKLNVLAGEIRETYGVETKVVRADFSQPGAAETVFAATEGLDMGFMSYVACLHSFGKIQDTPWEKHEAMINVNVVTFLKCFHHYMRIFAAQDRGAVINVSSMTGISSSPWNGQYGAGKAFILKMTEAVACECEGTGVDVEVITLGTTLTPSLLSNLPGGPQGEAVMKIALTPEECVDEAFEKLGKELSVIAGQRNKDSVHDWKANHTEDEYIRYMGSFYRD 263
                                    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 5GT9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GT9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GT9)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5GT9)

 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
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:201 - Pro A:202   [ 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
  5gt9
    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
  A4ECA9_9ACTN | A4ECA9
    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)
  (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
  A4ECA9_9ACTN | A4ECA9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A4ECA9_9ACTN | A4ECA9: 5fyd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5GT9)