Structure of PDB 3di1 Chain B Binding Site BS01

Receptor Information
>3di1 Chain B (length=291) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTHLFEGVGVALTTPFTNNKVNIEALKTHVNFLLENNAQAIIVNGTTAES
PTLTTDEKERILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGAD
AIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETV
EILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQR
GGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINP
IPIKALTSYLGFGNYELRLPLVSLEDTDTKVLRETYDTFKA
Ligand information
Ligand IDPYR
InChIInChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
InChIKeyLCTONWCANYUPML-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)C(O)=O
OpenEye OEToolkits 1.7.6CC(=O)C(=O)O
ACDLabs 12.01O=C(C(=O)O)C
FormulaC3 H4 O3
NamePYRUVIC ACID
ChEMBLCHEMBL1162144
DrugBankDB00119
ZINCZINC000001532517
PDB chain3di1 Chain B Residue 1002 [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]
PDB3di1 Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase
Resolution2.2 Å
Binding residue
(original residue number in PDB)		A11 G45 T46 T47 Y135 K163
Binding residue
(residue number reindexed from 1)		A11 G45 T46 T47 Y135 K163
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) T46 Y109 Y135 R140 K163 I206
Catalytic site (residue number reindexed from 1) T46 Y109 Y135 R140 K163 I206
Enzyme Commision number 4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.
Gene Ontology
Molecular Function
GO:0008840 4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0016829 lyase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
GO:0044281 small molecule metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3di1, PDBe:3di1, PDBj:3di1
PDBsum3di1
PubMed18671976
UniProtQ5HG25|DAPA_STAAC 4-hydroxy-tetrahydrodipicolinate synthase (Gene Name=dapA)

[Back to BioLiP]