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 :  3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE FROM RATTUS NORVEGICUS
 
Authors :  M. J. Bennett, B. P. Schlegel, J. M. Jez, T. M. Penning, M. Lewis
Date :  24 Feb 96  (Deposition) - 07 Dec 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Bennett, B. P. Schlegel, J. M. Jez, T. M. Penning, M. Lewis
Structure Of 3 Alpha-Hydroxysteroid/Dihydrodiol Dehydrogenase Complexed With Nadp+.
Biochemistry V. 35 10702 1996
PubMed-ID: 8718859  |  Reference-DOI: 10.1021/BI9604688
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.213
    Organ: LIVER
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: FORMERLY EC 1.1.1.50, HOWEVER A NEW CONVENTION DISTINGUISHES THIS AS AN A CLASS DEHYDROGENASE
    Strain: SPRAGUE-DAWLEY

 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:22 , THR A:23 , THR A:24 , ASP A:50 , TYR A:55 , LYS A:84 , HIS A:117 , SER A:166 , ASN A:167 , GLN A:190 , TYR A:216 , CYS A:217 , THR A:218 , LEU A:219 , GLY A:220 , SER A:221 , ALA A:253 , LEU A:268 , ARG A:270 , SER A:271 , PHE A:272 , ARG A:276 , GLU A:279 , HOH A:351BINDING SITE FOR RESIDUE NAP A 350
2AC2SOFTWAREGLY B:22 , THR B:23 , THR B:24 , ASP B:50 , TYR B:55 , LYS B:84 , HIS B:117 , SER B:166 , ASN B:167 , GLN B:190 , TYR B:216 , CYS B:217 , THR B:218 , LEU B:219 , GLY B:220 , SER B:221 , ALA B:253 , LEU B:268 , ARG B:270 , SER B:271 , PHE B:272 , ARG B:276 , GLU B:279 , HOH B:351BINDING SITE FOR RESIDUE NAP B 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LWI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LWI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LWI)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOKETO_REDUCTASE_1PS00798 Aldo/keto reductase family signature 1.DIDH_RAT45-62
 		  2A:45-62
B:45-62
2ALDOKETO_REDUCTASE_2PS00062 Aldo/keto reductase family signature 2.DIDH_RAT151-168
 		  2A:151-168
B:151-168
3ALDOKETO_REDUCTASE_3PS00063 Aldo/keto reductase family putative active site signature.DIDH_RAT268-283
 		  2A:268-283
B:268-283

(-) Exons   (9, 18)

Asymmetric/Biological Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000238351ENSRNOE00000169728chr17:77332903-77332778126DIDH_RAT1-28282A:1-26
B:1-26		26
26
1.2ENSRNOT000000238352ENSRNOE00000165296chr17:77328404-77328237168DIDH_RAT29-84562A:30-84
B:30-84		55
55
1.3ENSRNOT000000238353ENSRNOE00000226558chr17:77326224-77326108117DIDH_RAT85-123392A:85-123
B:85-123		39
39
1.4ENSRNOT000000238354ENSRNOE00000226521chr17:77324055-7732397878DIDH_RAT124-149262A:124-149
B:124-149		26
26
1.5ENSRNOT000000238355ENSRNOE00000277887chr17:77323455-77323333123DIDH_RAT150-190412A:150-190
B:150-190		41
41
1.6ENSRNOT000000238356ENSRNOE00000226508chr17:77321456-77321347110DIDH_RAT191-227372A:191-227 (gaps)
B:191-227 (gaps)		37
37
1.7ENSRNOT000000238357ENSRNOE00000226498chr17:77321080-77320915166DIDH_RAT227-282562A:227-282
B:227-282		56
56
1.8ENSRNOT000000238358ENSRNOE00000226492chr17:77319319-7731923783DIDH_RAT283-310282A:283-310
B:283-310		28
28
1.9ENSRNOT000000238359ENSRNOE00000170263chr17:77317784-773164591326DIDH_RAT310-322132A:310-311
B:310-311		2
2

(-) 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:305
 aligned with DIDH_RAT | P23457 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:311
                                    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       270       280       290       300       310 
             DIDH_RAT     1 MDSISLRVALNDGNFIPVLGFGTTVPEKVAKDEVIKATKIAIDNGFRHFDSAYLYEVEEEVGQAIRSKIEDGTVKREDIFYTSKLWSTFHRPELVRTCLEKTLKSTQLDYVDLYIIHFPMALQPGDIFFPRDEHGKLLFETVDICDTWEAMEKCKDAGLAKSIGVSNFNCRQLERILNKPGLKYKPVCNQVECHLYLNQSKMLDYCKSKDIILVSYCTLGSSRDKTWVDQKSPVLLDDPVLCAIAKKYKQTPALVALRYQLQRGVVPLIRSFNAKRIKELTQVFEFQLASEDMKALDGLNRNFRYNNAKYF 311
               SCOP domains d1lwia_ A: 3-alpha-hydroxy   steroid dehydrogenase                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1lwiA00 A:1-311 NADP-depen   dent oxidoreductase                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eee.....eee.eee.....---.hhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhh.....hhh.eeeeee.hhh..hhhhhhhhhhhhhhh......eeee...........................hhhhhhhhhhhhh.....eeee....hhhhhhhh..........eeeee.......hhhhhhhhhh..eeeee.....---..........hhh.hhhhhhhhhh...hhhhhhhhhhh....eee....hhhhhhhhhhhh....hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-26       Exon 1.2  PDB: A:30-84 UniProt: 29-84 [INCOMPLETE]      Exon 1.3  PDB: A:85-123 UniProt: 85-123Exon 1.4  PDB: A:124-149  Exon 1.5  PDB: A:150-190 UniProt: 150-190Exon 1.6  PDB: A:191-227 (gaps)      -------------------------------------------------------Exon 1.8  PDB: A:283-310    - Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:227-282 UniProt: 227-282               ---------------------------1. Transcript 1 (2)
                 1lwi A   1 MDSISLRVALNDGNFIPVLGFGTTVP---AKDEVIKATKIAIDNGFRHFDSAYLYEVEEEVGQAIRSKIEDGTVKREDIFYTSKLWSTFHRPELVRTCLEKTLKSTQLDYVDLYIIHFPMALQPGDIFFPRDEHGKLLFETVDICDTWEAMEKCKDAGLAKSIGVSNFNCRQLERILNKPGLKYKPVCNQVECHLYLNQSKMLDYCKSKDIILVSYCTLGS---KTWVDQKSPVLLDDPVLCAIAKKYKQTPALVALRYQLQRGVVPLIRSFNAKRIKELTQVFEFQLASEDMKALDGLNRNFRYNNAKYF 311
                                    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       270       280       290       300       310 
                                                    26  30                                                                                                                                                                                            221 225                                                                                      


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with DIDH_RAT | P23457 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:311
                                    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       270       280       290       300       310 
             DIDH_RAT     1 MDSISLRVALNDGNFIPVLGFGTTVPEKVAKDEVIKATKIAIDNGFRHFDSAYLYEVEEEVGQAIRSKIEDGTVKREDIFYTSKLWSTFHRPELVRTCLEKTLKSTQLDYVDLYIIHFPMALQPGDIFFPRDEHGKLLFETVDICDTWEAMEKCKDAGLAKSIGVSNFNCRQLERILNKPGLKYKPVCNQVECHLYLNQSKMLDYCKSKDIILVSYCTLGSSRDKTWVDQKSPVLLDDPVLCAIAKKYKQTPALVALRYQLQRGVVPLIRSFNAKRIKELTQVFEFQLASEDMKALDGLNRNFRYNNAKYF 311
               SCOP domains d1lwib_ B: 3-alpha-hydroxy   steroid dehydrogenase                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1lwiB00 B:1-311 NADP-depen   dent oxidoreductase                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----------------Aldo_ket_   red-1lwiB01 B:18-301                                                                                                                                                                                                                                                            ---------- Pfam domains (1)
           Pfam domains (2) -----------------Aldo_ket_   red-1lwiB02 B:18-301                                                                                                                                                                                                                                                            ---------- Pfam domains (2)
         Sec.struct. author ..hhh.eee.....eee.eee.....---.hhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhh.....hhh.eeeeee.hhh..hhhhhhhhhhhhhhh......eeee...........................hhhhhhhhhhhhh.....eeee....hhhhhhhh..........eeeee.......hhhhhhhhhh..eeeee.....---..........hhh.hhhhhhhhhh...hhhhhhhhhhh..eeeee....hhhhhhhhhhhh....hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:1-26       Exon 1.2  PDB: B:30-84 UniProt: 29-84 [INCOMPLETE]      Exon 1.3  PDB: B:85-123 UniProt: 85-123Exon 1.4  PDB: B:124-149  Exon 1.5  PDB: B:150-190 UniProt: 150-190Exon 1.6  PDB: B:191-227 (gaps)      -------------------------------------------------------Exon 1.8  PDB: B:283-310    - Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:227-282 UniProt: 227-282               ---------------------------1. Transcript 1 (2)
                 1lwi B   1 MDSISLRVALNDGNFIPVLGFGTTVP---AKDEVIKATKIAIDNGFRHFDSAYLYEVEEEVGQAIRSKIEDGTVKREDIFYTSKLWSTFHRPELVRTCLEKTLKSTQLDYVDLYIIHFPMALQPGDIFFPRDEHGKLLFETVDICDTWEAMEKCKDAGLAKSIGVSNFNCRQLERILNKPGLKYKPVCNQVECHLYLNQSKMLDYCKSKDIILVSYCTLGS---KTWVDQKSPVLLDDPVLCAIAKKYKQTPALVALRYQLQRGVVPLIRSFNAKRIKELTQVFEFQLASEDMKALDGLNRNFRYNNAKYF 311
                                    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       270       280       290       300       310 
                                                    26  30                                                                                                                                                                                            221 225
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Aldo_ket_red] (94)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DIDH_RAT | P23457)
molecular function
    GO:0047042    androsterone dehydrogenase (B-specific) activity    Catalysis of the reaction: NAD(P)+ + androsterone = NAD(P)H + H+ + 5-alpha-androstane-3,17-dione. The reaction is B-specific (i.e. the pro-S hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD(P)+.
    GO:0047023    androsterone dehydrogenase activity    Catalysis of the reaction: NAD(P)+ + androsterone = NAD(P)H + H+ + 5-alpha-androstane-3,17-dione.
    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.
    GO:0016229    steroid dehydrogenase activity    Catalysis of an oxidation-reduction (redox) reaction in which one substrate is a sterol derivative.
biological process
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    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:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
(no "Cis Peptide Bonds" information available for 1lwi)
 

(-) 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
  1lwi
    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
  DIDH_RAT | P23457
    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)
  1.1.1.213
    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
  DIDH_RAT | P23457
    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
        DIDH_RAT | P23457: 1afs 1ral

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LWI)