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Crystal structure of a putative carveol dehydrogenase from mycobacterium paratuberculosis bound to nicotinamide adenine dinucleotide

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

PDB: 3PGX
Type: protein
Length: 1,080 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carveol dehydrogenase
UniProt: Q73SC8
Ligands: NAD
Pockets: 15 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Carveol dehydrogenase	protein	270	49% helix, 16% strand	Q73SC8

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	469	0.84	0.91	70	NAD
2	1122	0.84	0.85	68	empty
3	482	0.83	0.90	69	NAD
4	457	0.83	0.90	61	NAD
5	442	0.82	0.89	59	NAD

Interfaces

6 interfaces between chains.

A–C · 1763 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1757 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1222 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1204 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 420 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3PGX · Crystal structure of a putative carveol dehydrogenase from Mycobacterium paratuberculosis… · the same entry in another collection · chain A against A, TM-score 1.00
Q73SC8 · AlphaFold monomer V2.0 prediction for uncharacterized NAD-dependent oxidoreductase… · 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 Q73SC8
Elsewhere: RCSB PDB 3PGX · PDBe 3PGX · UniProt Q73SC8

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