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Crystal structure of a short chain dehydrogenase from mycobacterium smegmatis

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

PDB: 3O38
Type: protein
Length: 969 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short chain dehydrogenase
UniProt: A0R4Z8
Ligands: NA
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Short chain dehydrogenase	protein	244	45% helix, 15% strand	A0R4Z8
B	Short chain dehydrogenase	protein	240	46% helix, 15% strand	A0R4Z8
C	Short chain dehydrogenase	protein	241	46% helix, 15% strand	A0R4Z8

Ligands and binding sites

NA · Sodium ion · metal · chains C

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

Pockets

9 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	708	0.70	0.77	72	empty
2	712	0.70	0.77	70	empty
3	172	0.58	0.82	33	empty
4	200	0.53	0.78	32	empty
5	181	0.50	0.78	29	empty

Interfaces

6 interfaces between chains.

B–C · 2044 Å² buried · 35 hydrogen bonds · protein-protein
A–D · 1982 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 1732 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1720 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 227 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3O38 · Crystal structure of a short chain dehydrogenase from Mycobacterium smegmatis · 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 A0R4Z8
Elsewhere: RCSB PDB 3O38 · PDBe 3O38 · UniProt A0R4Z8

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