Structure of PDB 1wdm Chain A Binding Site BS01

Receptor Information

>1wdm Chain A (length=707) Species: 296 (Pseudomonas fragi)

MIYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKAD
ASVKGVIVSSGKDVFIVGADITEFVENFKLPDAELIAGNLEANKIFSDFE
DLNVPTVAAINGIALGGGLEMCLAADFRVMADSAKIGLPEVKLGIYPGFG
GTVRLPRLIGVDNAVEWIASGKENRAEDALKVSAVDAVVTADKLGAAALD
LIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGFVAGQAGPNYP
APVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNCLIGLFLNDQEL
KKKAKVYDKIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGI
EQGLAEAAKLLVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEA
VVENPKVKQAVLAEVENHVREDAILASNTSTISISLLAKALKRPENFVGM
HFFNPVHMMPLVEVIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGFLV
NRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGH
HGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYKKLVDSSV
LEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGL
VYGIGFPLFRGGALRYIDSIGVAEFVALADQYAELGALYHPTAKLREMAK
NGQSFFG

Ligand information

• Ligand ID: ACO
• InChI: InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
• InChIKey: ZSLZBFCDCINBPY-ZSJPKINUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.341: 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
  ACDLabs 10.04: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)C
  CACTVS 3.341: 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
  OpenEye OEToolkits 1.5.0: 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
• Formula: C23 H38 N7 O17 P3 S
• Name: ACETYL COENZYME *A
• ChEMBL: CHEMBL1230809
• ZINC: ZINC000008551095
• PDB chain: 1wdm Chain A Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1wdm Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): K142 D297 M459 N501 P534 Y660 L666
• Binding residue (residue number reindexed from 1): K142 D297 M459 N501 P534 Y652 L658
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): A69 N89 N93 G117 E120 P139 E140 P147 G148 S430 H451 E463 N501
• Catalytic site (residue number reindexed from 1): A69 N89 N93 G117 E120 P139 E140 P147 G148 S430 H451 E463 N501
• Enzyme Commision number: 1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase.
  4.2.1.17: enoyl-CoA hydratase.
  5.1.2.3: 3-hydroxybutyryl-CoA epimerase.
  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:0005515 protein binding
• GO:0008692 3-hydroxybutyryl-CoA epimerase activity
• GO:0016491 oxidoreductase 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:0070403 NAD+ binding

Biological Process

• GO:0006631 fatty acid metabolic process
• GO:0006635 fatty acid beta-oxidation
• GO:0009056 catabolic process
• GO:0009062 fatty acid catabolic process
• GO:0016042 lipid catabolic process

Cellular Component

• GO:0036125 fatty acid beta-oxidation multienzyme complex

External links

• PDB: RCSB:1wdm, PDBe:1wdm, PDBj:1wdm
• PDBsum: 1wdm
• PubMed: 15229654
• UniProt: P28793|FADB_PSEFR Fatty acid oxidation complex subunit alpha (Gene Name=fadB)