Structure of PDB 6pd2 Chain A Binding Site BS01

Receptor Information
>6pd2 Chain A (length=615) Species: 243275 (Treponema denticola ATCC 35405) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIKQAVILAGGLGSRLKDKTKTMPKGFLEIGGTAIVEQSVQKLLAHGIEK
IVIGTGHCNEYYDNLAKKYPAIITVKNENYANTGSMGTLEVCASFVNESF
LLLESDLIYDSAGLFSLINDERKNLILASGATKSGDEVYLEADEKNCLTG
LSKNRDALKNIFGELVGITKLTKSTLDKMCAYAKIHHSDLPKMEYEHALL
EAAKTIPVAIKRIEYFVWREIDNEDHLEMAVKNIYPHIVENEKLRAVRRE
VLLNPGPATTTDSVKYAQVSADICPREKAFGDLMQWLCDELKLFALASET
NPDEYETVMFGCSGTGADEVMVSSCVPDTGRLLVIDNGSYGARMAKIADI
YKIPMDIFKSSTYEPLDLQKLEAEFATKKYTHLACVYHETTTGLLNPLHI
ICPMAKKYGMVTIVDAVSAYCGMPMDLKSLGIDFMASTSNKNIQGMAGVG
FVICNKAELEKTKDYPMRNYYLNLYDQYAYFAKTHQTRFTPPVQTMYALR
QAVLETKQETVQKRYERYTACWNILVAAIKKLGLKMLVKEEHQSHFITAI
LEPETPKYSFEALHDFAAEHSFTIYPGKLGNIDTFRIANIGDIQPEEMRR
FTVKLKEYMNGIGVG
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 chain6pd2 Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6pd2 The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		S313 G314 T315 Y340 T390 D415 V417 K441
Binding residue
(residue number reindexed from 1)		S313 G314 T315 Y340 T390 D415 V417 K441
Annotation score1
Enzymatic activity
Enzyme Commision number 2.6.1.37: 2-aminoethylphosphonate--pyruvate transaminase.
2.7.7.107: (2-aminoethyl)phosphonate cytidylyltransferase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
GO:0047304 2-aminoethylphosphonate-pyruvate transaminase activity
Biological Process
GO:0019700 organic phosphonate catabolic process
GO:0032923 organic phosphonate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pd2, PDBe:6pd2, PDBj:6pd2
PDBsum6pd2
PubMed31420548
UniProtQ73MU2|PNTCW_TREDE Bifunctional 2-aminoethylphosphonate cytidylyltransferase/aminotransferase (Gene Name=pntC)

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