Structure of PDB 6jqm Chain A Binding Site BS01

Receptor Information

>6jqm Chain A (length=678) Species: 83333 (Escherichia coli K-12)

QQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEK
GAPALRAMTFIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIE
GGIGTLFTYASLGSRELPDDTLWPEDELIPLSKEGGFAARHLLTSKSGVA
VHINAFNFPCWGMLEKLAPTWLGGMPAIIKPATATAQLTQAMVKSIVDSG
LVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQPNIVAKSI
PFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRI
IVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVN
ILLAAGCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVA
TLMPAQNQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQI
LNEESAKESTGHGSPLPQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQG
SPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGDSLLTPRRTMTEAD
IVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDAGVG
PVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEW
AVEVFNQHQTPVALYSILTLVARQHGDF

Ligand information

• Ligand ID: NDP
• InChI: InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: ACFIXJIJDZMPPO-NNYOXOHSSA-N
• SMILES:
  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)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
• Formula: C21 H30 N7 O17 P3
• Name: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
• ChEMBL: CHEMBL407009
• DrugBank: DB02338
• ZINC: ZINC000008215411
• PDB chain: 6jqm Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6jqm Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): R20 I154 N155 A156 F157 N158 K181 A183 T184 G232 S233 T236 A257 D258 C295 E395 F397
• Binding residue (residue number reindexed from 1): R19 I153 N154 A155 F156 N157 K180 A182 T183 G231 S232 T235 A256 D257 C294 E394 F396
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N158 E256 C295 L484
• Catalytic site (residue number reindexed from 1): N157 E255 C294 L483
• Enzyme Commision number: 1.2.1.91: 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase.
  3.3.2.12: oxepin-CoA hydrolase.

Gene Ontology

Molecular Function

• GO:0004300 enoyl-CoA hydratase activity
• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
• GO:0016726 oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
• GO:0016787 hydrolase activity
• GO:0016803 ether hydrolase activity
• GO:0016823 hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances
• GO:0016829 lyase activity
• GO:0042802 identical protein binding

Biological Process

• GO:0010124 phenylacetate catabolic process

External links

• PDB: RCSB:6jqm, PDBe:6jqm, PDBj:6jqm
• PDBsum: 6jqm
• PubMed: 31511507
• UniProt: P77455|PAAZ_ECOLI Bifunctional protein PaaZ (Gene Name=paaZ)