Structure of PDB 5esd Chain A Binding Site BS01

Receptor Information
>5esd Chain A (length=539) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLH
VRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPL
IVLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALN
ATWRSATCRVLAAATGARTANAGPVHFDIPLREPLVPTPPGRPAGKPWTY
TPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNP
LHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVS
GNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHV
AAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTV
STAIGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPI
PRSLTIVVSNDNGGGIFELLSDVSSRIFGTPHDVDVGALCRAYHVESRQI
EVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain5esd Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5esd Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		D440 D469 G471
Binding residue
(residue number reindexed from 1)		D432 D461 G463
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C26 E55
Catalytic site (residue number reindexed from 1) C26 E55
Enzyme Commision number 2.2.1.9: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016740 transferase activity
GO:0030145 manganese ion binding
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
GO:0070204 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity
Biological Process
GO:0009234 menaquinone biosynthetic process
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5esd, PDBe:5esd, PDBj:5esd
PDBsum5esd
PubMed27291649
UniProtP9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

[Back to BioLiP]