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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  K154 CIRCULAR PERMUTATION OF OLD YELLOW ENZYME
 
Authors :  J. R. Horton, A. B. Daugherty, X. Cheng, S. Lutz
Date :  26 Oct 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Circular Permutation, Catalysis, Old Yellow Enzyme, Flavin Cofactor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Daugherty, J. R. Horton, X. Cheng, S. Lutz
Structural And Functional Consequences Of Circular Permutation On The Active Site Of Old Yellow Enzyme
Acs Catalysis V. 5 892 2015
PubMed: search

(-) Compounds

Molecule 1 - NADPH DEHYDROGENASE 1
    Chains: A, B
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-14B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 154-397, 2-153
    Gene: OYE1
    Organism Common: LAGER YEAST
    Organism Scientific: SACCHAROMYCES PASTORIANUS
    Organism Taxid: 27292
    Synonym: OLD YELLOW ENZYME 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:40 , ASN A:43 , ARG A:92 , GLY A:173 , ASN A:174 , GLY A:196 , ARG A:197 , PHE A:223 , PRO A:282 , PRO A:283 , LEU A:284 , THR A:285 , GLY A:320 , GLN A:362 , HOH A:623 , HOH A:704 , HOH A:795 , HOH A:950 , HOH A:957BINDING SITE FOR RESIDUE FMN A 501
2AC2SOFTWAREASN A:28 , GLU A:339BINDING SITE FOR RESIDUE EDO A 502
3AC3SOFTWAREALA A:228 , ASP A:233 , TRP B:300 , HOH B:630BINDING SITE FOR RESIDUE EDO A 503
4AC4SOFTWAREHIS A:229 , ASP A:233 , HOH A:986BINDING SITE FOR RESIDUE EDO A 504
5AC5SOFTWAREASP A:233 , GLU A:239BINDING SITE FOR RESIDUE EDO A 505
6AC6SOFTWAREHIS B:40 , ASN B:43 , ARG B:92 , PRO B:144 , ASN B:174 , GLY B:196 , ARG B:197 , PHE B:223 , PRO B:282 , PRO B:283 , LEU B:284 , THR B:285 , GLY B:320 , GLN B:362 , HOH B:634 , HOH B:667 , HOH B:737 , HOH B:964 , HOH B:1072BINDING SITE FOR RESIDUE FMN B 501
7AC7SOFTWARETYR B:162 , ARG B:171 , HOH B:785BINDING SITE FOR RESIDUE EDO B 502
8AC8SOFTWAREHIS B:229 , ASP B:233 , HOH B:935 , HOH B:1167BINDING SITE FOR RESIDUE EDO B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:291 -Pro A:292
2His B:291 -Pro B:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RNX)

(-) 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:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhh.hhhhhhhhhhhhhhhhhhh.....eeeee.....................hhhhhhh...eeee.....hhhhhhhhh....eeee.hhhhhhh.hhhhhhhhh......hhhhh............hhhhhhhh..................hhhhh.eee..eee...ee...................hhhhhhhhhh.....eee...ee...............hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh...eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rnx A   3 ANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWGTSSFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLWVLGWAAFPDNLARDGLRYDSASDNVFMD 392
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392


Chain B from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhh.hhhhhhhhhhhhhhhhhhh.....eeeee.....................hhhhhhh...eeee.....hhhhhhhhh....eeee.hhhhhhh.hhhhhhhhh......hhhhh............hhhhhhhh..................hhhhh.eee..eee...ee...................hhhhhhhhhh.....eee...ee...............hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh...eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rnx B   3 ANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWGTSSFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLWVLGWAAFPDNLARDGLRYDSASDNVFMD 392
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
   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 4RNX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:291 - Pro A:292   [ RasMol ]  
    His B:291 - Pro B:292   [ RasMol ]  
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4rnx
    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 4k7v 4k7y 4k8e 4k8h 4rnu 4rnv 4rnw 4yil 4ync

(-) Related Entries Specified in the PDB File

4rnu 4rnv 4rnw