Structure of PDB 5x8f Chain A Binding Site BS02

Receptor Information
>5x8f Chain A (length=483) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEQPNWLMQRAQLTPERIALIYEDQTVTFAELFAASKRMAEQLAAHSVRK
GDTAAILLQNRAEMVYAVHACFLLGVKAVLLNTKLSTHERLFQLEDSGSG
FLLTDSSFEKKEYEHIVQTIDVDELMKEAAEEIEIEAYMQMDATATLMYT
SGTTGKPKGVQQTFGNHYFSAVSSALNLGITEQDRWLIALPLFHISGLSA
LFKSVIYGMTVVLHQRFSVSDVLHSINRHEVTMISAVQTMLASLLEETNR
CPESIRCILLGGGPAPLPLLEECREKGFPVFQSYGMTETCSQIVTLSPEF
SMEKLGSAGKPLFSCEIKIERDGQVCEPYEHGEIMVKGPNVMKSYFNRES
ANEASFQNGWLKTGDLGYLDNEGFLYVLDRRSDLIISGGENIYPAEVESV
LLSHPAVAEAGVSGAEDKKWGKVPHAYLVLHKPVSAGELTDYCKERLAKY
KRPKKFFVLDRLPRNASNKLLRNQLKDARKGEL
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain5x8f Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5x8f Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode
Resolution1.763 Å
Binding residue
(original residue number in PDB)		T152 G265 P266 S285 Y286 G287 M288 T289 D367 N393
Binding residue
(residue number reindexed from 1)		T150 G263 P264 S283 Y284 G285 M286 T287 D365 N391
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) T152 S172 H196 T289 E290 I388 N393 K471
Catalytic site (residue number reindexed from 1) T150 S170 H194 T287 E288 I386 N391 K469
Enzyme Commision number 6.2.1.26: o-succinylbenzoate--CoA ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008756 o-succinylbenzoate-CoA ligase activity
GO:0016405 CoA-ligase activity
GO:0016874 ligase activity
Biological Process
GO:0009234 menaquinone biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5x8f, PDBe:5x8f, PDBj:5x8f
PDBsum5x8f
PubMed28559280
UniProtP23971|MENE_BACSU 2-succinylbenzoate--CoA ligase (Gene Name=menE)

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