Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  TROPINONE REDUCTASE-I COMPLEX WITH NADP
 
Authors :  K. Nakajima, A. Yamashita, H. Akama, T. Nakatsu, H. Kato, T. Hashimoto, J. Oda, Y. Yamada
Date :  23 Oct 97  (Deposition) - 18 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Oxidoreductase, Tropane Alkaloid Biosynthesis, Reduction Of Tropinone To Tropine, Short-Chain Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Nakajima, A. Yamashita, H. Akama, T. Nakatsu, H. Kato, T. Hashimoto, J. Oda, Y. Yamada
Crystal Structures Of Two Tropinone Reductases: Different Reaction Stereospecificities In The Same Protein Fold.
Proc. Natl. Acad. Sci. Usa V. 95 4876 1998
PubMed-ID: 9560196  |  Reference-DOI: 10.1073/PNAS.95.9.4876
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TROPINONE REDUCTASE-I
    Cell LineBL21
    ChainsA, B
    EC Number1.1.1.236
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPETTR1
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorPET21D
    Expression System Vector TypePLASMID
    OrganCULTURED ROOT
    Organism CommonJIMSONWEED
    Organism ScientificDATURA STRAMONIUM
    Organism Taxid4076

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:28 , SER A:30 , LYS A:31 , GLY A:32 , ILE A:33 , SER A:52 , ARG A:53 , ASN A:54 , CYS A:77 , ASP A:78 , LEU A:79 , ASN A:106 , ALA A:107 , LEU A:156 , SER A:157 , SER A:158 , TYR A:171 , LYS A:175 , PRO A:201 , GLY A:202 , ILE A:204 , HOH A:296BINDING SITE FOR RESIDUE NAP A 274
2AC2SOFTWAREGLY B:28 , SER B:30 , LYS B:31 , GLY B:32 , ILE B:33 , SER B:52 , ARG B:53 , GLU B:57 , CYS B:77 , ASP B:78 , LEU B:79 , ASN B:106 , ALA B:107 , LEU B:156 , SER B:157 , SER B:158 , TYR B:171 , LYS B:175 , PRO B:201 , GLY B:202 , ILE B:204 , THR B:206 , LEU B:208 , VAL B:209 , HOH B:278 , HOH B:290 , HOH B:292 , HOH B:296BINDING SITE FOR RESIDUE NAP B 274

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AE1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AE1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AE1)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.TRN1_DATST158-186
 
  2A:158-186
B:158-186
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.TRN1_DATST158-186
 
  2A:158-186
B:158-186
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.TRN1_DATST158-186
 
  4A:158-186
B:158-186

(-) Exons   (0, 0)

(no "Exon" information available for 1AE1)

(-) 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:245
 aligned with TRN1_DATST | P50162 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:258
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265        
           TRN1_DATST    16 RWSLKGTTALVTGGSKGIGYAIVEELAGLGARVYTCSRNEKELDECLEIWREKGLNVEGSVCDLLSRTERDKLMQTVAHVFDGKLNILVNNAGVVIHKEAKDFTEKDYNIIMGTNFEAAYHLSQIAYPLLKASQNGNVIFLSSIAGFSALPSVSLYSASKGAINQMTKSLACEWAKDNIRVNSVAPGVILTPLVETAIKKNPHQKEEIDNFIVKTPMGRAGKPQEVSALIAFLCFPAASYITGQIIWADGGFTANGGF 273
               SCOP domains d1ae1a_ A: Tropinone reductase                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ae1A00 A:16-273 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh......eeee..............hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeeee..hhh.......hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....-------------hhhhhhhhhhh........hhhhhhhhhhhh.hhh......eeee...hhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:158-186    --------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ae1 A  16 RWSLKGTTALVTGGSKGIGYAIVEELAGLGARVYTCSRNEKELDECLEIWREKGLNVEGSVCDLLSRTERDKLMQTVAHVFDGKLNILVNNAGVVIHKEAKDFTEKDYNIIMGTNFEAAYHLSQIAYPLLKASQNGNVIFLSSIAGFSALPSVSLYSASKGAINQMTKSLACEWAKDNIRVNSVAPGVIL-------------QKEEIDNFIVKTPMGRAGKPQEVSALIAFLCFPAASYITGQIIWADGGFTANGGF 273
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         -   |   225       235       245       255       265        
                                                                                                                                                                                                                       205           219                                                      

Chain B from PDB  Type:PROTEIN  Length:258
 aligned with TRN1_DATST | P50162 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:258
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265        
           TRN1_DATST    16 RWSLKGTTALVTGGSKGIGYAIVEELAGLGARVYTCSRNEKELDECLEIWREKGLNVEGSVCDLLSRTERDKLMQTVAHVFDGKLNILVNNAGVVIHKEAKDFTEKDYNIIMGTNFEAAYHLSQIAYPLLKASQNGNVIFLSSIAGFSALPSVSLYSASKGAINQMTKSLACEWAKDNIRVNSVAPGVILTPLVETAIKKNPHQKEEIDNFIVKTPMGRAGKPQEVSALIAFLCFPAASYITGQIIWADGGFTANGGF 273
               SCOP domains d1ae1b_ B: Tropinone reductase                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ae1B00 B:16-273 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh......eeee..............hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeeee..hhh.......hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhh.hhh......eeee...hhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:158-186    --------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ae1 B  16 RWSLKGTTALVTGGSKGIGYAIVEELAGLGARVYTCSRNEKELDECLEIWREKGLNVEGSVCDLLSRTERDKLMQTVAHVFDGKLNILVNNAGVVIHKEAKDFTEKDYNIIMGTNFEAAYHLSQIAYPLLKASQNGNVIFLSSIAGFSALPSVSLYSASKGAINQMTKSLACEWAKDNIRVNSVAPGVILTPLVETAIKKNPHQKEEIDNFIVKTPMGRAGKPQEVSALIAFLCFPAASYITGQIIWADGGFTANGGF 273
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265        

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AE1)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRN1_DATST | P50162)
molecular function
    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:0050356    tropine dehydrogenase activity    Catalysis of the reaction: NADP(+) + tropine = H(+) + NADPH + tropinone.
biological process
    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:0009710    tropane alkaloid biosynthetic process    The chemical reactions and pathways resulting in the breakdown of tropane alkaloids, compounds containing the 8-methyl-8-azabicyclo(3.2.1)octane ring system.

 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
    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 1ae1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ae1
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TRN1_DATST | P50162
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.236
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TRN1_DATST | P50162
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1AE1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AE1)