Structure of PDB 3dod Chain B Binding Site BS02

Receptor Information
>3dod Chain B (length=416) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSV
WLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKK
LTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKSYKAPIPYVY
RSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEG
YLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGI
TGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENL
ALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSK
ETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEM
VAIMKQAIHEVTSLED
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 chain3dod Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3dod Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .
Resolution1.9 Å
Binding residue
(original residue number in PDB)		W54 S112 G113 A114 D251 V253 K280
Binding residue
(residue number reindexed from 1)		W51 S109 G110 A111 D219 V221 K248
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F17 E217 D251 A254 K280 A417
Catalytic site (residue number reindexed from 1) F14 E185 D219 A222 K248 A385
Enzyme Commision number 2.6.1.105: lysine--8-amino-7-oxononanoate transaminase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004015 adenosylmethionine-8-amino-7-oxononanoate transaminase activity
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009102 biotin biosynthetic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dod, PDBe:3dod, PDBj:3dod
PDBsum3dod
PubMed20565114
UniProtP53555|BIOK_BACSU L-Lysine--8-amino-7-oxononanoate transaminase (Gene Name=bioK)

[Back to BioLiP]