MolNFT v1 · #98119 · protein

Crystal structure of a putative short chain dehydrogenase from mycobacterium smegmatis

4KZP · Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family…: “Crystal structure of a putative short chain dehydrogenase from mycobacterium smegmatis”. X-ray diffraction, 18 pockets (best druggability 0.76). MolNFT v1 #98119 on…

PDB: 4KZP
Type: protein
Length: 1,161 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein
EC: 1.1.1.100
UniProt: A0R4P1
Pockets: 18 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein (EC 1.1.1.100)	protein	291	45% helix, 16% strand	A0R4P1
B	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein (EC 1.1.1.100)	protein	283	45% helix, 18% strand	A0R4P1
C	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein (EC 1.1.1.100)	protein	295	46% helix, 17% strand	A0R4P1
D	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein (EC 1.1.1.100)	protein	292	45% helix, 17% strand	A0R4P1

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 13 copies · chains A, D, C, B
GOL · Glycerol · additive · 4 copies · chains A, C, D

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1091	0.76	0.79	98	EDO, GOL
2	71	0.75	0.99	24	empty
3	64	0.73	0.99	25	empty
4	344	0.66	0.81	48	empty
5	386	0.63	0.78	39	EDO

Interfaces

5 interfaces between chains.

B–C · 4122 Å² buried · 58 hydrogen bonds · protein-protein
A–D · 4029 Å² buried · 56 hydrogen bonds · protein-protein
B–D · 214 Å² buried · 1 hydrogen bond · protein-protein
A–C · 177 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 19 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4KZP · Crystal Structure of a Putative 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 A0R4P1
Elsewhere: RCSB PDB 4KZP · PDBe 4KZP · UniProt A0R4P1

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