Structure of PDB 3zwa Chain B Binding Site BS01

Receptor Information

>3zwa Chain B (length=721) Species: 10116 (Rattus norvegicus)

GSHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKA
IVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVA
LGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVA
LDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRI
FNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVG
IKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVS
SVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEA
SRAHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSA
LCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPS
RYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEE
GSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGT
PVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLST
FLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDV
IYLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYL
RRLVAQGSPPLKEWQSLAGPH

Ligand information

• Ligand ID: 3H9
• InChI: InChI=1S/C27H46N7O18P3S/c1-4-5-15(35)10-18(37)56-9-8-29-17(36)6-7-30-25(40)22(39)27(2,3)12-49-55(46,47)52-54(44,45)48-11-16-21(51-53(41,42)43)20(38)26(50-16)34-14-33-19-23(28)31-13-32-24(19)34/h13-16,20-22,26,35,38-39H,4-12H2,1-3H3,(H,29,36)(H,30,40)(H,44,45)(H,46,47)(H2,28,31,32)(H2,41,42,43)/p-4/t15-,16+,20+,21+,22-,26+/m0/s1
• InChIKey: VAAHKRMGOFIORX-IKTBLOROSA-J
• SMILES:
  CACTVS 3.370: CCC[CH](O)CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P]([O-])(=O)O[P]([O-])(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P]([O-])([O-])=O)n2cnc3c(N)ncnc23
  CACTVS 3.370: CCC[C@H](O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P]([O-])([O-])=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.7.2: CCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])O)O
  OpenEye OEToolkits 1.7.2: CCCC(CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)([O-])OP(=O)([O-])OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])O)O
• Formula: C27 H42 N7 O18 P3 S
• Name: (S)-3-Hydroxyhexanoyl-CoA
• PDB chain: 3zwa Chain B Residue 1720

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3zwa The Isomerase and Hydratase Reaction Mechanism of the Crotonase Active Site of the Multifunctional Enzyme (Type-1), as Deduced from Structures of Complexes with 3S-Hydroxy- Acyl-Coa.
• Resolution: 2.47 Å
• Binding residue (original residue number in PDB): P20 A59 G60 A61 D62 I63 F66 L73 G100 E103 P122 E123 L126 F271 K275 K279
• Binding residue (residue number reindexed from 1): P23 A62 G63 A64 D65 I66 F69 L76 G103 E106 P125 E126 L129 F274 K278 K282
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): A61 F66 G76 G100 E103 P122 E123 P130 G131 K249 S410 H431 E443 N481
• Catalytic site (residue number reindexed from 1): A64 F69 G79 G103 E106 P125 E126 P133 G134 K252 S413 H434 E446 N484
• Enzyme Commision number: 1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase.
  4.2.1.17: enoyl-CoA hydratase.
  5.3.3.8: Delta(3)-Delta(2)-enoyl-CoA isomerase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity
• GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity
• GO:0004300 enoyl-CoA hydratase activity
• GO:0016491 oxidoreductase activity
• GO:0016509 long-chain-3-hydroxyacyl-CoA dehydrogenase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0016829 lyase activity
• GO:0016853 isomerase activity
• GO:0016863 intramolecular oxidoreductase activity, transposing C=C bonds
• GO:0019899 enzyme binding
• GO:0070403 NAD+ binding

Biological Process

• GO:0006631 fatty acid metabolic process
• GO:0006635 fatty acid beta-oxidation

Cellular Component

• GO:0005777 peroxisome
• GO:0005829 cytosol

External links

• PDB: RCSB:3zwa, PDBe:3zwa, PDBj:3zwa
• PDBsum: 3zwa
• PubMed: 23351063
• UniProt: P07896|ECHP_RAT Peroxisomal bifunctional enzyme (Gene Name=Ehhadh)