Structure of PDB 3zwb Chain A Binding Site BS01

Receptor Information

>3zwb Chain A (length=725) Species: 10116 (Rattus norvegicus)

PRGSHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTV
KAIVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQG
VALGGGLELALGCHYRIANAKARVGLPAVTLGILPGARGTQLLPRVVGVP
VALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPR
RIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYE
VGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQP
VSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEK
EASRAHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAEL
SALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVI
PSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLL
EEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPP
GTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWL
STFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHI
DVIYLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSD
YLRRLVAQGSPPLKEWQSLAGPHGS

Ligand information

• Ligand ID: TC6
• InChI: InChI=1S/C27H44N7O17P3S/c1-4-5-6-7-18(36)55-11-10-29-17(35)8-9-30-25(39)22(38)27(2,3)13-48-54(45,46)51-53(43,44)47-12-16-21(50-52(40,41)42)20(37)26(49-16)34-15-33-19-23(28)31-14-32-24(19)34/h6-7,14-16,20-22,26,37-38H,4-5,8-13H2,1-3H3,(H,29,35)(H,30,39)(H,43,44)(H,45,46)(H2,28,31,32)(H2,40,41,42)/p-4/b7-6+/t16-,20-,21-,22+,26-/m1/s1
• InChIKey: OINXHIBNZUUIMR-IXUYQXAASA-J
• SMILES:
  OpenEye OEToolkits 1.7.2: CCC/C=C/C(=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
  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
  CACTVS 3.370: CCCC=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=C/C(=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
• Formula: C27 H40 N7 O17 P3 S
• Name: (2E)-Hexenoyl-CoA
• PDB chain: 3zwb Chain A Residue 1723

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3zwb 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: 3.1 Å
• Binding residue (original residue number in PDB): P20 V21 A23 A59 G60 A61 D62 I63 V96 L98 G100 E103 G131 Y156 K275
• Binding residue (residue number reindexed from 1): P25 V26 A28 A64 G65 A66 D67 I68 V101 L103 G105 E108 G136 Y161 K280
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): A61 G76 G100 E103 P122 A123 P130 G131 S410 H431 E443 N481
• Catalytic site (residue number reindexed from 1): A66 G81 G105 E108 P127 A128 P135 G136 S415 H436 E448 N486
• 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:3zwb, PDBe:3zwb, PDBj:3zwb
• PDBsum: 3zwb
• PubMed: 23351063
• UniProt: P07896|ECHP_RAT Peroxisomal bifunctional enzyme (Gene Name=Ehhadh)