MolNFT v1 · #28524 · protein

Crystal structure of D-3-phosphoglycerate dehydrogenase from mycobacterium tuberculosis

1YGY: “Crystal structure of D-3-phosphoglycerate dehydrogenase from mycobacterium tuberculosis”. X-ray diffraction, 9 pockets (best druggability 0.82). MolNFT v1 #28524 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YGY
Type: protein
Length: 1,054 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-3-phosphoglycerate dehydrogenase
EC: 1.1.1.95
UniProt: P0A544
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)	protein	527	33% helix, 25% strand	P0A544

Ligands and binding sites

TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	828	0.82	0.85	65	empty
2	1030	0.78	0.80	105	empty
3	318	0.54	0.75	50	empty
4	73	0.48	0.83	18	empty
5	132	0.48	0.78	35	empty

Interfaces

1 interface between chains.

A–B · 2637 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

1YGY · Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0A544
Elsewhere: RCSB PDB 1YGY · PDBe 1YGY · UniProt P0A544

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