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 :  OYE1-W116A COMPLEXED WITH (R)-CARVONE
 
Authors :  B. Sullivan, Y. A. Pompeu, J. D. Stewart
Date :  17 Apr 13  (Deposition) - 09 Oct 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Old Yellow Enzyme, Carvone, Oxidoreductase, Tim Barrel, Nadph Dehydrogenase 1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. A. Pompeu, B. Sullivan, J. D. Stewart
X‑ Ray Crystallography Reveals How Subtle Changes Control The Orientation Of Substrate Binding In An Alkene Reductase
Acs Catalysis V. 3 2376 2013
PubMed: search  |  Reference-DOI: 10.1021/CS400622E

(-) Compounds

Molecule 1 - NADPH DEHYDROGENASE 1
    Chains: A
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3B
    Expression System Strain: BL21-GOLD (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OYE1
    Mutation: YES
    Organism Common: LAGER YEAST
    Organism Scientific: SACCHAROMYCES PASTORIANUS
    Organism Taxid: 27292
    Synonym: OLD YELLOW ENZYME 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric Unit (6, 7)
No.NameCountTypeFull Name
107V1Ligand/Ion(5R)-2-METHYL-5-(PROP-1-EN-2-YL)CYCLOHEX-2-EN-1-ONE
21PE1Ligand/IonPENTAETHYLENE GLYCOL
3CL1Ligand/IonCHLORIDE ION
4FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
5MG1Ligand/IonMAGNESIUM ION
6NA2Ligand/IonSODIUM ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
107V2Ligand/Ion(5R)-2-METHYL-5-(PROP-1-EN-2-YL)CYCLOHEX-2-EN-1-ONE
21PE2Ligand/IonPENTAETHYLENE GLYCOL
3CL-1Ligand/IonCHLORIDE ION
4FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
5MG-1Ligand/IonMAGNESIUM ION
6NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:34 , PRO A:35 , LEU A:36 , THR A:37 , GLY A:72 , GLN A:114 , HIS A:191 , ASN A:194 , ARG A:243 , PRO A:295 , GLY A:324 , ASN A:325 , GLY A:347 , ARG A:348 , 07V A:404 , HOH A:506 , HOH A:512 , HOH A:517 , HOH A:823BINDING SITE FOR RESIDUE FMN A 401
2AC2SOFTWAREHOH A:931 , HOH A:932 , HOH A:939 , HOH A:956BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREASP A:83 , ASN A:126BINDING SITE FOR RESIDUE CL A 403
4AC4SOFTWARETHR A:37 , TYR A:82 , ALA A:116 , HIS A:191 , ASN A:194 , TYR A:196 , TYR A:375 , FMN A:401BINDING SITE FOR RESIDUE 07V A 404
5AC5SOFTWARETYR A:375 , 1PE A:406BINDING SITE FOR RESIDUE NA A 405
6AC6SOFTWAREMET A:39 , PHE A:123 , TYR A:375 , NA A:405BINDING SITE FOR RESIDUE 1PE A 406
7AC7SOFTWAREASP A:372 , TYR A:375 , GLN A:376 , HOH A:703BINDING SITE FOR RESIDUE NA A 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K7V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His A:43 -Pro A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K7V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K7V)

(-) Exons   (0, 0)

(no "Exon" information available for 4K7V)

(-) 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:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4k7va_ A: Old yellow enzyme (OYE)                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh.eee..eee...ee...................hhhhhhhhhh.....eee...ee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh....ee.......hhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhh.hhhhhhhhhhhhhhhhhhh.....eeeee.....................hhhhhhh...eeee.....hhhhhhhhh....eeee.hhhhhhh.hhhhhhhhh......hhhhh............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k7v A   1 SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLAVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK 399
                                    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       320       330       340       350       360       370       380       390
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K7V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K7V)

(-) Gene Ontology  (7, 7)

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
    07V  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:43 - Pro A:44   [ RasMol ]  
 
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
  4k7v
    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
  OYE1_SACPS | Q02899
    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)
  1.6.99.1
    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
  OYE1_SACPS | Q02899
    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
        OYE1_SACPS | Q02899: 1bwk 1bwl 1k02 1k03 1oya 1oyb 1oyc 3rnd 3tx9 3txz 4gbu 4ge8 4gwe 4gxm 4h4i 4h6k 4k7y 4k8e 4k8h 4rnu 4rnv 4rnw 4rnx 4yil 4ync

(-) Related Entries Specified in the PDB File

3rnd
3tx9
3txz OYE1-W116Q COMPLEXED WITH (R)-CARVONE
4gbu OYE1-W116A COMPLEXED WITH THE AROMATIC PRODUCT OF (S)- CARVONE DISMUTATION
4ge8 OYE1-W116I COMPLEXED WITH (S)-CARVONE
4gwe OYE1-W116L COMPLEXED WITH (R)-CARVONE
4gxm OYE1-W116L COMPLEXED WITH THE AROMATIC PRODUCT OF (R)- CARVONE DISMUTATION
4h4i OYE1-W116V COMPLEXED WITH THE AROMATIC PRODUCT OF (S)- CARVONE DISMUTATION
4h6k OYE1-W116I
4k7y OYE1-W116T
4k8e OYE1-W116V COMPLEXED WITH THE AROMATIC PRODUCT OF (R)- CARVONE DISMUTATION
4k8h OYE1-W116V COMPLEXED WITH (R)-CARVONE