Structure of PDB 6tnm Chain A Binding Site BS01

Receptor Information

>6tnm Chain A (length=719) Species: 83333 (Escherichia coli K-12)

MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQS
DLKGLLLRSNKAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLED
LPVPTIAAVNGYALGGGCECVLATDYRLATPDLRIGLPETKLGIMPGFGG
SVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVKAEKLVEGAKAV
LRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMVAQTAGKHYPA
PITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK
GKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLT
LGMTEAAKLLNKQLERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAV
VENPKVKKAVLAETEQKVRQDTVLASNTSTIPISELANALERPENFCGMH
FFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKMGKTPIVVNDCPGFFVN
RVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYLLDVVGIDTAH
HAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP
KKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIAT
PAEADMALVYGLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYEVP
EGLRNKARHNEPYYPPVEP

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 6tnm Chain A Residue 802

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tnm Insights into the stability and substrate specificity of the E. coli aerobic beta-oxidation trifunctional enzyme complex.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): D343 I344 V400 V401 V406 K584
• Binding residue (residue number reindexed from 1): D343 I344 V400 V401 V406 K584
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): A68 F73 G116 E119 P138 E139 G147 N271 S429 H450 E462 N500
• Catalytic site (residue number reindexed from 1): A68 F73 G116 E119 P138 E139 G147 N271 S429 H450 E462 N500
• 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:0008692 3-hydroxybutyryl-CoA epimerase 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: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:6tnm, PDBe:6tnm, PDBj:6tnm
• PDBsum: 6tnm
• PubMed: 32171906
• UniProt: P21177|FADB_ECOLI Fatty acid oxidation complex subunit alpha (Gene Name=fadB)