Structure of PDB 2jlc Chain A Binding Site BS03

Receptor Information

>2jlc Chain A (length=554) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MSVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTPLTLAAAENSAFIHH
THFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKL
ILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVS
TIDHALGTLHAGGVHINCPFAEPLYMDDTGLSWQQRLGDWWQDDKPWLRE
APRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIGDV
LSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQASCE
PEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIPRL
AEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDALSQ
LPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLNAL
ALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHAAA
MFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLLAQ
VSHL

Ligand information

Ligand ID

TPP

InChI

InChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1

InChIKey

AYEKOFBPNLCAJY-UHFFFAOYSA-O

SMILES

Software	SMILES
CACTVS 3.341	Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0	Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0	Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341	Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N

Formula

C12 H19 N4 O7 P2 S

Name

THIAMINE DIPHOSPHATE

PDB chain

2jlc Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2jlc Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase).
Resolution	2.5 Å
Binding residue (original residue number in PDB)	P30 E55
Binding residue (residue number reindexed from 1)	P30 E55
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	A29 E55
Catalytic site (residue number reindexed from 1)	A29 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:0003824	catalytic activity
GO:0016740	transferase activity
GO:0030145	manganese ion binding
GO:0030976	thiamine pyrophosphate binding
GO:0042803	protein homodimerization activity
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

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Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:2jlc, PDBe:2jlc, PDBj:2jlc
PDBsum	2jlc
PubMed	18983854
UniProt	P17109\|MEND_ECOLI 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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