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 :  CRYSTALS STRUCTURE OF ACYL-COA OXIDASE-2 IN CAENORHABDITIS ELEGANS BOUND WITH FAD, ASCAROSIDE-COA, AND ATP
 
Authors :  X. Zhang, K. Li, R. A. Jones, S. D. Bruner, R. A. Butcher
Date :  19 May 16  (Deposition) - 24 Aug 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dauer Pheromone; Ascarosides; B-Oxidation; Atp; Crystal Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhang, K. Li, R. A. Jones, S. D. Bruner, R. A. Butcher
Structural Characterization Of Acyl-Coa Oxidases Reveals A Direct Link Between Pheromone Biosynthesis And Metabolic State In Caenorhabditis Elegans.
Proc. Natl. Acad. Sci. Usa V. 113 10055 2016
PubMed-ID: 27551084  |  Reference-DOI: 10.1073/PNAS.1608262113

(-) Compounds

Molecule 1 - ACYL-COENZYME A OXIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ACOX-2, CELE_F08A8.2, F08A8.2
    Mutation: YES
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
16QA2Ligand/Ion~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL] 5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MG2Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:113 , TYR A:147 , GLN A:149 , THR A:150 , GLY A:155 , SER A:156 , TRP A:187 , PRO A:188 , GLY A:189 , THR A:430 , GLU A:434 , MET A:436 , VAL A:437 , 6QA A:703 , HOH A:801 , HOH A:833 , ARG B:318 , GLN B:320 , VAL B:332 , TYR B:335 , THR B:337 , GLN B:338 , ARG B:341 , ALA B:406 , GLY B:408 , GLY B:409 , HOH B:816 , HOH B:861binding site for residue FAD A 701
2AC2SOFTWARESER A:390 , HIS A:394 , ASN A:435 , MET A:436 , LEU A:439 , ARG A:525 , ARG A:528 , TYR A:573 , HOH A:828 , HIS B:340 , ARG B:341 , GLN B:402 , TYR B:565 , MG B:701 , HOH B:842binding site for residue ATP A 702
3AC3SOFTWARELEU A:117 , TYR A:147 , GLN A:149 , GLY A:155 , SER A:156 , LEU A:158 , ARG A:159 , PHE A:243 , HIS A:281 , LYS A:283 , TYR A:286 , MET A:289 , ARG A:293 , GLU A:299 , HIS A:382 , TYR A:431 , ALA A:432 , GLY A:433 , VAL A:437 , GLN A:441 , ARG A:444 , FAD A:701binding site for residue 6QA A 703
4AC4SOFTWAREATP A:702 , ASP B:569binding site for residue MG B 701
5AC5SOFTWAREARG A:318 , VAL A:332 , TYR A:335 , THR A:337 , GLN A:338 , ARG A:341 , ALA A:406 , GLY A:408 , GLY A:409 , LEU B:113 , TYR B:147 , GLN B:149 , THR B:150 , GLY B:155 , SER B:156 , TRP B:187 , PRO B:188 , GLY B:189 , THR B:430 , GLY B:433 , GLU B:434 , MET B:436 , VAL B:437 , 6QA B:705 , HOH B:832binding site for residue FAD B 702
6AC6SOFTWAREHIS A:340 , ARG A:341 , GLN A:402 , TYR A:565 , ASP A:569 , SER B:390 , HIS B:394 , ASN B:435 , MET B:436 , LEU B:439 , ARG B:525 , ARG B:528 , TYR B:573 , MG B:704 , HOH B:808 , HOH B:813 , HOH B:844binding site for residue ATP B 703
7AC7SOFTWAREATP B:703binding site for residue MG B 704
8AC8SOFTWAREALA B:116 , LEU B:117 , GLN B:149 , GLY B:155 , SER B:156 , LEU B:158 , ARG B:159 , PHE B:243 , LYS B:283 , TYR B:286 , MET B:289 , ARG B:293 , GLU B:299 , HIS B:382 , TYR B:431 , ALA B:432 , GLY B:433 , VAL B:437 , MET B:438 , GLN B:441 , ARG B:444 , LYS B:448 , FAD B:702binding site for residue 6QA B 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K3J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K3J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K3J)

(-) Exons   (0, 0)

(no "Exon" information available for 5K3J)

(-) 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:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee........hhhhh..eeeee....eeeee.......eeeee.......eeeeeeeee....eeeeeeeeee............eeeee...........eeeeee..eeee.hhh.....ee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhh...hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k3j A   3 NRSIRDGDNPELLEERRMATFDTDKMAAVIYGSEEFARRRREITDAVSKIPELADIKPYPFLTREEKVTEGTRKISILTKYLNQLIDRDNEEESLHLHREVIGYEGHPFALHDALFIPTLQSQASDEQQEKWLERARRREIIGCYAQTELGHGSNLRNLETTAVYDIASQEFVLHTPTTTALKWWPGALGKSCNYALVVAELIIKRNNYGPHFFMVQLRDEKTHIPLKGVTVGDIGPKMNFNAADNGYLGLNNLRVPRTNLLMRHCKVEADGTYVKPPHAKIGYSGMVKIRSQMAMEQGLFLAHALTIAARYSAVRRQGHLDDKQVEVKVLDYQTQQHRLFPSLARAYAFIFTGFETIHLYSQLLKDVDMGNTSGMADLHALTSGLKSVVAHETGEGIEQARMACGGHGYSMASYISVVYGIAIGGCTYAGENMVMLLQLARYLVKSVELIKAGKAKKLGPVASYLADKSDETDLTSLNGYVKMFENMARRQAWKATEKFLKLMESGESREVAWNKSAVELTRASRLHTRLFIIEAFMRRVSRIEDIPVKEVLTDLLHLHVNYELLDVATYALEFMSFTQLDYVRDQLYLYLEKIRPNAVSLVDSFQISDMQLRSVLGRRDGHVYENLFKWAKSSPLNNADVLPSVEKYLKPMMEKAKLAAA 664
                                    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       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662  


Chain B from PDB  Type:PROTEIN  Length:659
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee........hhhhh..eeeee....eeeee.......eeeee.......eeeeeeee..eeeeeeee............eeeee...........eeeeee..eeee.hhh.....ee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhh...hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k3j B   2 ANRSIRDGDNPELLEERRMATFDTDKMAAVIYGSEEFARRRREITDAVSKIPELADIKPYPFLTREEKVTEGTRKISILTKYLNQLIDRDNEEESLHLHREVIGYEGHPFALHDALFIPTLQSQASDEQQEKWLERARRREIIGCYAQTELGHGSNLRNLETTAVYDIASQEFVLHTPTTTALKWWPGALGKSCNYALVVAELNYGPHFFMVQLRDEKTHIPLKGVTVGDIGPKMNFNAADNGYLGLNNLRVPRTNLLMRHCKVEADGTYVKPPHAKIGYSGMVKIRSQMAMEQGLFLAHALTIAARYSAVRRQGHLDDKQVEVKVLDYQTQQHRLFPSLARAYAFIFTGFETIHLYSQLLKDVDMGNTSGMADLHALTSGLKSVVAHETGEGIEQARMACGGHGYSMASYISVVYGIAIGGCTYAGENMVMLLQLARYLVKSVELIKAGKAKKLGPVASYLADKSDETDLTSLNGYVKMFENMARRQAWKATEKFLKLMESGESREVAWNKSAVELTRASRLHTRLFIIEAFMRRVSRIEDIPVKEVLTDLLHLHVNYELLDVATYALEFMSFTQLDYVRDQLYLYLEKIRPNAVSLVDSFQISDMQLRSVLGRRDGHVYENLFKWAKSSPLNNADVLPSVEKYLKPMMEKAKLAAAH 665
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  ||   216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656         
                                                                                                                                                                                                                                    204|                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                     210
   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 5K3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K3J)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    6QA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
(no "Cis Peptide Bonds" information available for 5k3j)
 

(-) 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
  5k3j
    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
  O62137_CAEEL | O62137
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  O62137_CAEEL | O62137
    Protein Disorder Prediction: DisEMBL | 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 5K3J)

(-) Related Entries Specified in the PDB File

5k3g 5k3h 5k3i