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Retinal dehydrogenase type two with NAD bound

Analyse Retinal dehydrogenase type two with NAD bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BI9
Type: protein
Length: 1,917 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinal dehydrogenase type II
EC: 1.2.1.-
UniProt: Q63639
Ligands: NAD, CL
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinal dehydrogenase type II (EC 1.2.1.-)	protein	478	41% helix, 21% strand	Q63639
B	Retinal dehydrogenase type II (EC 1.2.1.-)	protein	477	40% helix, 19% strand	Q63639
C	Retinal dehydrogenase type II (EC 1.2.1.-)	protein	480	40% helix, 22% strand	Q63639
D	Retinal dehydrogenase type II (EC 1.2.1.-)	protein	482	40% helix, 21% strand	Q63639

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 2 copies · chains 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	679	0.84	0.88	55	empty
2	192	0.81	0.96	37	empty
3	694	0.80	0.84	78	empty
4	111	0.79	0.97	20	empty
5	220	0.78	0.92	39	empty

Interfaces

6 interfaces between chains.

C–D · 2086 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1984 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1632 Å² buried · 41 hydrogen bonds · protein-protein
A–D · 1603 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 848 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1BI9 · Retinal dehydrogenase type two with NAD bound · the same entry in another collection · chain D against D, TM-score 1.00
Q63639 · AlphaFold monomer V2.0 prediction for retinal dehydrogenase 2 (Q63639) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q63639
Elsewhere: RCSB PDB 1BI9 · PDBe 1BI9 · UniProt Q63639

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