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Crystal structure of phosphoglycerate dehydrogenase from pyrococcus horikoshii OT3

Analyse Crystal structure of phosphoglycerate dehydrogenase from pyrococcus horikoshii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WWK
Type: protein
Length: 606 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoglycerate dehydrogenase
EC: 1.1.1.95
Ligands: NAD
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoglycerate dehydrogenase (EC 1.1.1.95)	protein	304	40% helix, 17% strand	—
B	Phosphoglycerate dehydrogenase (EC 1.1.1.95)	protein	302	42% helix, 18% strand	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	466	0.63	0.77	51	NAD
2	380	0.63	0.78	48	NAD
3	86	0.39	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 2510 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

1WWK · Crystal structure of phosphoglycerate dehydrogenase from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00

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

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