MolNFT v1 · #159640 · protein

Structure of the NADH-bound form of 20BETA-hydroxysteroid dehydrogenase from bifidobacterium adolescentis strain L2-32

6OW4 · Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family…: “Structure of the NADH-bound form of 20BETA-hydroxysteroid dehydrogenase from bifidobacterium adolescentis…”. X-ray diffraction, 1 ligand (NAD), 18 pockets (best…

PDB: 6OW4
Type: protein
Length: 2,227 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein
UniProt: A7A7R9
Ligands: NAD
Pockets: 18 · best druggability 0.86

Structure

x-ray diffraction · 7 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein	protein	278	48% helix, 15% strand	A7A7R9
B, D	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein	protein	274	48% helix, 16% strand	A7A7R9
C	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein	protein	277	48% helix, 14% strand	A7A7R9
E	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein	protein	280	50% helix, 15% strand	A7A7R9
F	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein	protein	284	51% helix, 16% strand	A7A7R9
G	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein	protein	277	49% helix, 16% strand	A7A7R9
H	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein	protein	283	49% helix, 14% strand	A7A7R9

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

18 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	1029	0.86	0.87	53	empty
2	944	0.84	0.85	72	NAD
3	1183	0.82	0.83	78	NAD
4	579	0.75	0.81	47	NAD
5	519	0.72	0.81	52	NAD

Interfaces

14 interfaces between chains.

A–E · 3369 Å² buried · 48 hydrogen bonds · protein-protein
B–F · 3221 Å² buried · 48 hydrogen bonds · protein-protein
A–F · 1656 Å² buried · 38 hydrogen bonds · protein-protein
D–G · 1649 Å² buried · 38 hydrogen bonds · protein-protein
B–E · 1628 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

6OW4 · Structure of the NADH-bound form of 20beta-Hydroxysteroid Dehydrogenase from… · the same entry in another collection · 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 A7A7R9
Elsewhere: RCSB PDB 6OW4 · PDBe 6OW4 · UniProt A7A7R9

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