Structure of PDB 3ddn Chain B Binding Site BS01

Receptor Information
>3ddn Chain B (length=525) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRS
ATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHS
AAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGR
IGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISV
HLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVR
AAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRL
ALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQ
VRGELAAEEVEVLRLSALRGLFSAVIEVTFVNAPALAAERGVTAEICKAS
ESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQG
INLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQ
DVPDDVRTAIAAAVDAYKLEVVDLS
Ligand information
Ligand IDHPV
InChIInChI=1S/C3H5O7P/c4-2(3(5)6)1-10-11(7,8)9/h1H2,(H,5,6)(H2,7,8,9)
InChIKeyLFLUCDOSQPJJBE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C(=O)C(=O)O)OP(=O)(O)O
CACTVS 3.341OC(=O)C(=O)CO[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCC(=O)C(=O)O
FormulaC3 H5 O7 P
Name2-oxo-3-(phosphonooxy)propanoic acid;
Hydroxypyruvic acid phosphate
ChEMBL
DrugBank
ZINCZINC000003869279
PDB chain3ddn Chain B Residue 600 [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]
PDB3ddn Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R72 V75 N99 A283 Q289
Binding residue
(residue number reindexed from 1)		R70 V73 N97 A281 Q287
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) N99 R233 D257 E262 H280
Catalytic site (residue number reindexed from 1) N97 R231 D255 E260 H278
Enzyme Commision number 1.1.1.399: 2-oxoglutarate reductase.
1.1.1.95: phosphoglycerate dehydrogenase.
Gene Ontology
Molecular Function
GO:0004617 phosphoglycerate dehydrogenase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
Biological Process
GO:0006564 L-serine biosynthetic process
Cellular Component
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ddn, PDBe:3ddn, PDBj:3ddn
PDBsum3ddn
PubMed18627175
UniProtP9WNX3|SERA_MYCTU D-3-phosphoglycerate dehydrogenase (Gene Name=serA)

[Back to BioLiP]