Structure of PDB 4elw Chain D Binding Site BS01

Receptor Information
>4elw Chain D (length=265) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PDEAMLYAPVEWHDCSEGFEDIRYEKSTDGIAKITINRPQVRNAFRPLTV
KEMIQALADARYDDNIGVIILTGAGDKAFCSGGDQLNVLDFQRQIRTCPK
PVVAMVAGYSIGGGHVLHMMCDLTIAADNAIFGQTGPKVGSFDGGWGASY
MARIVGQKKAREIWFLCRQYDAKQALDMGLVNTVVPLADLEKETVRWCRE
MLQNSPMALRCLKAALNADCDGQAGLQELAGNATMLFYMTEEGQEGRNAF
NQKRQPDFSKFKRNP
Ligand information
Ligand IDNO3
InChIInChI=1S/NO3/c2-1(3)4/q-1
InChIKeyNHNBFGGVMKEFGY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341		[O-][N+]([O-])=O
OpenEye OEToolkits 1.5.0[N+](=O)([O-])[O-]
FormulaN O3
NameNITRATE ION
ChEMBLCHEMBL186200
DrugBankDB14049
ZINC
PDB chain4elw Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4elw Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways
Resolution2.551 Å
Binding residue
(original residue number in PDB)		G132 G133 Q154 T155 G156
Binding residue
(residue number reindexed from 1)		G112 G113 Q134 T135 G136
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G86 L109 G133 V136 G156 S161 D163 G164 A250 Y258
Catalytic site (residue number reindexed from 1) G83 L89 G113 V116 G136 S141 D143 G144 A230 Y238
Enzyme Commision number 4.1.3.36: 1,4-dihydroxy-2-naphthoyl-CoA synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008935 1,4-dihydroxy-2-naphthoyl-CoA synthase activity
GO:0016829 lyase activity
GO:0071890 bicarbonate binding
Biological Process
GO:0009234 menaquinone biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4elw, PDBe:4elw, PDBj:4elw
PDBsum4elw
PubMed22606952
UniProtP0ABU0|MENB_ECOLI 1,4-dihydroxy-2-naphthoyl-CoA synthase (Gene Name=menB)

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