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The X-ray crystal structure of eta-crystallin

Analyse The X-ray crystal structure of eta-crystallin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1O9J
Type: protein
Length: 1,976 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase, cytosolic 1
EC: 1.2.1.3
UniProt: Q28399
Ligands: NAD
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aldehyde dehydrogenase, cytosolic 1 (EC 1.2.1.3)	protein	494	41% helix, 22% strand	Q28399

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains D
DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains B

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1174	0.91	0.93	118	empty
2	817	0.86	0.88	122	NAD
3	1003	0.85	0.85	123	NAD
4	604	0.82	0.87	75	NAD
5	179	0.81	0.96	35	empty

Interfaces

6 interfaces between chains.

C–D · 2897 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 2833 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 1557 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 1529 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 1071 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1O9J · The X-ray crystal structure of eta-crystallin · the same entry in another collection · chain D against D, TM-score 1.00
Q28399 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, cytosolic 1 (Q28399) · a predicted model of the same protein · chain D 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 Q28399
Elsewhere: RCSB PDB 1O9J · PDBe 1O9J · UniProt Q28399

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