Structure of PDB 2jlc Chain B Binding Site BS02

Receptor Information

>2jlc Chain B (length=556) 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
TIDHALGTLHAGGVHINCPFAEPLYGEMDDTGLSWQQRLGDWWQDDKPWL
REAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIG
DVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQAS
CEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIP
RLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDAL
SQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLN
ALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHA
AAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLL
AQVSHL

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)	S391 L392 I418 D419 G441 D442 L443 S444 Y447 N469 G471 G472 Q473 I474
Binding residue (residue number reindexed from 1)	S391 L392 I418 D419 G441 D442 L443 S444 Y447 N469 G471 G472 Q473 I474
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

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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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