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Second apo form of an NADP dependent aldehyde dehydrogenase with GLU250 situated 3.7 a from CYS284

Analyse Second apo form of an NADP dependent aldehyde dehydrogenase with GLU250… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QI6
Type: protein
Length: 1,896 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (NADP dependent nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase)
EC: 1.2.1.9
UniProt: Q59931
Ligands: SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein (NADP dependent nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase) (EC 1.2.1.9)	protein	474	42% helix, 23% strand	Q59931

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1106	0.84	0.85	93	empty
2	1069	0.83	0.84	93	empty
3	607	0.79	0.84	71	empty
4	173	0.72	0.90	29	empty
5	195	0.70	0.88	31	empty

Interfaces

6 interfaces between chains.

C–D · 2508 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2505 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 1147 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1138 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 795 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1QI6 · Second apo form of an NADP dependent aldehyde dehydrogenase with GLU250 situated 3.7 a… · the same entry in another collection · chain D against D, TM-score 1.00
Q59931 · AlphaFold monomer V2.0 prediction for NADP-dependent glyceraldehyde-3-phosphate… · a predicted model of the same protein · 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 Q59931
Elsewhere: RCSB PDB 1QI6 · PDBe 1QI6 · UniProt Q59931

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