Structure of PDB 2x7j Chain B Binding Site BS02

Receptor Information

>2x7j Chain B (length=579) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQ
IDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIV
LTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTL
ASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGT
QSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILA
DPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPV
FLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAA
TRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLF
VGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPV
TLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTH
FEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIE
IKTDRQSRVQLHRDMLNEAVREVKKQWEL

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

2x7j 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	2x7j Structure and Reactivity of Bacillus Subtilis Mend Catalyzing the First Committed Step in Menaquinone Biosynthesis.
Resolution	2.35 Å
Binding residue (original residue number in PDB)	S405 M406 I433 D434 G456 D457 L458 S459 N484 G486 G487 G488 I489 F490
Binding residue (residue number reindexed from 1)	S404 M405 I432 D433 G455 D456 L457 S458 N483 G485 G486 G487 I488 F489
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	C28 E54
Catalytic site (residue number reindexed from 1)	C27 E53
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: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:2x7j, PDBe:2x7j, PDBj:2x7j
PDBsum	2x7j
PubMed	20600129
UniProt	P23970\|MEND_BACSU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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