Structure of PDB 1mdz Chain A Binding Site BS02

Receptor Information
>1mdz Chain A (length=364) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DFLPFSRPAMGAEELAAVKTVLDSGWITTGPKNQELEAAFCRLTGNQYAV
AVSSATAGMHIALMALGIGEGDEVITPSMTWVSTLNMIVLLGANPVMVDV
DRDTLMVTPEHIEAAITPQTKAIIPVHYAGAPADLDAIYALGERYGIPVI
EDAAHATGTSYKGRHIGARGTAIFSFHAIKNITCAEGGIVVTDNPQFADK
LRSLKFHGLGVDQAEVLAPGYKYNLPDLNAAIALAQLQKLDALNARRAAI
AAQYHQAMADLPFQPLSLPSWEHIHAWHLFIIRVDEARCGITRDALMASL
KTKGIGTGLHFRAAHTQKYYRERFPTLTLPDTEWNSERICSLPLFPDMTE
SDFDRVITALHQIA
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain1mdz Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1mdz Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: A 4-amino-4-deoxy-L-arabinose lipopolysaccharide modifying enzyme
Resolution2.07 Å
Binding residue
(original residue number in PDB)		A63 T64 W89 D160 A162 H163 S183 K188
Binding residue
(residue number reindexed from 1)		A55 T56 W81 D152 A154 H155 S175 K180
Annotation score1
Enzymatic activity
Enzyme Commision number 2.6.1.87: UDP-4-amino-4-deoxy-L-arabinose aminotransferase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
GO:0099620 UDP-4-amino-4-deoxy-L-arabinose aminotransferase
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009245 lipid A biosynthetic process
GO:0046493 lipid A metabolic process
GO:0046677 response to antibiotic

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1mdz, PDBe:1mdz, PDBj:1mdz
PDBsum1mdz
PubMed12429098
UniProtQ8ZNF3|ARNB_SALTY UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase (Gene Name=arnB)

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