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Crystal structure of a putative short chain dehydrogenase or reductase from mycobacterium abscessus

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

PDB: 3RIH
Type: protein
Length: 1,039 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short chain dehydrogenase or reductase
UniProt: B1MJ88
Ligands: K
Pockets: 7 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Short chain dehydrogenase or reductase	protein	260	47% helix, 16% strand	B1MJ88
C	Short chain dehydrogenase or reductase	protein	259	47% helix, 16% strand	B1MJ88

Ligands and binding sites

K · Potassium ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, D, C
PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 4 copies · chains A, D, B, C

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

Pockets

7 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	1052	0.86	0.87	90	EDO
2	626	0.72	0.79	50	PG5, EDO
3	557	0.72	0.80	46	PG5, EDO
4	570	0.70	0.79	49	PG5, EDO
5	545	0.70	0.79	44	PG5, EDO

Interfaces

6 interfaces between chains.

A–C · 1829 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1826 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1610 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1580 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 825 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3RIH · Crystal structure of a putative short chain dehydrogenase or 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 B1MJ88
Elsewhere: RCSB PDB 3RIH · PDBe 3RIH · UniProt B1MJ88

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