Structure of PDB 2d3t Chain A Binding Site BS01

Receptor Information

>2d3t Chain A (length=708) Species: 296 (Pseudomonas fragi)

MIYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKAD
ASVKGVIVSSGKDVFIVGADITEFVENFKLPDAELIAGNLEANKIFSDFE
DLNVPTVAAINGIALGGGLEMCLAADFRVMADSAKIGLPEVKLGIYPGFG
GTVRLPRLIGVDNAVEWIASGKENRAEDALKVSAVDAVVTADKLGAAALD
LIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGFVAGQAGPNYP
APVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNCLIGLFLNDQEL
KKKAKVYDKIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGI
EQGLAEAAKLLVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEA
VVENPKVKQAVLAEVENHVREDAILASNTSTISISLLAKALKRPENFVGM
HFFNPVHMMPLVEVIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGFLV
NRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGH
HGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEKKLVDSS
VLEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMG
LVYGIGFPLFRGGALRYIDSIGVAEFVALADQYAELGALYHPTAKLREMA
KNGQSFFG

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 2d3t Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2d3t Ligand-Induced Domain Rearrangement of Fatty Acid beta-Oxidation Multienzyme Complex
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): I324 M325 K343 D344 V401 E403 V411 S430
• Binding residue (residue number reindexed from 1): I324 M325 K343 D344 V401 E403 V411 S430
• Annotation score: 4

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:2d3t, PDBe:2d3t, PDBj:2d3t
• PDBsum: 2d3t
• PubMed: 16472743
• UniProt: P28793|FADB_PSEFR Fatty acid oxidation complex subunit alpha (Gene Name=fadB)