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Glyceraldehyde-3-phosphate dehydrogenase mutant with asp 32 replaced by gly, leu 187 replaced by ala, and pro 188 replaced by ser complexed with NADP+

Analyse Glyceraldehyde-3-phosphate dehydrogenase mutant with asp 32 replaced by gly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DBV
Type: protein
Length: 1,336 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase
EC: 1.2.1.12
UniProt: P00362
Ligands: NDP, SO4
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O, P, Q, R	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12)	protein	334	28% helix, 30% strand	P00362

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains O, R, P, Q
SO4 · Sulfate ion · ion · 8 copies · chains O, P, Q, R

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.76	0.98	29	empty
2	711	0.71	0.78	62	SO4, NDP
3	650	0.70	0.78	54	SO4, NDP
4	660	0.70	0.78	65	SO4, NDP
5	648	0.69	0.78	58	SO4, NDP

Interfaces

6 interfaces between chains.

Q–R · 2121 Å² buried · 38 hydrogen bonds · protein-protein
O–P · 2095 Å² buried · 35 hydrogen bonds · protein-protein
P–Q · 1428 Å² buried · 23 hydrogen bonds · protein-protein
O–R · 1419 Å² buried · 16 hydrogen bonds · protein-protein
P–R · 590 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2DBV · Glyceraldehyde-3-phosphate dehydrogenase mutant with asp 32 replaced by gly, leu 187… · the same entry in another collection · chain R against R, TM-score 1.00
P00362 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P00362) · a predicted model of the same protein · chain R 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 P00362
Elsewhere: RCSB PDB 2DBV · PDBe 2DBV · UniProt P00362

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