Research workbench

Crystal structure of a putative short-chain DEHYDROGENASE/REDUCTASE from mycobacterium abscessus bound to NAD

Analyse Crystal structure of a putative short-chain DEHYDROGENASE/REDUCTASE from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S55
Type: protein
Length: 2,164 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative short-chain DEHYDROGENASE/REDUCTASE
UniProt: B1MLR7
Ligands: NAD, CA
Pockets: 16 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	269	49% helix, 15% strand	B1MLR7
B	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	270	49% helix, 16% strand	B1MLR7
C	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	269	47% helix, 16% strand	B1MLR7
D, F	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	275	46% helix, 15% strand	B1MLR7
E	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	266	47% helix, 16% strand	B1MLR7
H	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	271	48% helix, 15% strand	B1MLR7

Ligands and binding sites

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

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1161	0.87	0.88	120	NAD
2	1178	0.87	0.88	125	NAD
3	1186	0.86	0.87	127	NAD
4	1157	0.86	0.86	126	NAD
5	121	0.80	0.97	27	empty

Interfaces

14 interfaces between chains.

E–F · 1652 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1637 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1632 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1628 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 1417 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

3S55 · Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium… · 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 B1MLR7
Elsewhere: RCSB PDB 3S55 · PDBe 3S55 · UniProt B1MLR7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.