MolNFT v1 · #81133 · protein

Crystal structure of a probable glycerol dehydrogenase from sinorhizobium meliloti 1021

3UHJ: “Crystal structure of a probable glycerol dehydrogenase from sinorhizobium meliloti 1021”. X-ray diffraction, 2 ligands (ZN, SE), 20 pockets (best druggability 0.76). MolNFT v1 #81133 on GenesisL1: 3D structure, binding sites and…

PDB: 3UHJ
Type: protein
Length: 2,842 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable glycerol dehydrogenase
EC: 1.1.1.6
UniProt: Q92MR2
Ligands: ZN, SE
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 7 distinct chains · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable glycerol dehydrogenase (EC 1.1.1.6)	protein	357	54% helix, 13% strand	Q92MR2
B, G	Probable glycerol dehydrogenase (EC 1.1.1.6)	protein	356	57% helix, 12% strand	Q92MR2
C	Probable glycerol dehydrogenase (EC 1.1.1.6)	protein	355	57% helix, 13% strand	Q92MR2
D	Probable glycerol dehydrogenase (EC 1.1.1.6)	protein	357	56% helix, 13% strand	Q92MR2
E	Probable glycerol dehydrogenase (EC 1.1.1.6)	protein	355	56% helix, 13% strand	Q92MR2
F	Probable glycerol dehydrogenase (EC 1.1.1.6)	protein	351	57% helix, 14% strand	Q92MR2
H	Probable glycerol dehydrogenase (EC 1.1.1.6)	protein	355	56% helix, 12% strand	Q92MR2

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
SE · Selenium atom · ion · 2 copies · chains E, H
GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, G

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	733	0.76	0.81	76	empty
2	659	0.74	0.80	90	GOL
3	414	0.73	0.83	59	GOL
4	475	0.73	0.82	59	GOL
5	465	0.72	0.82	68	GOL

Interfaces

9 interfaces between chains.

A–B · 1550 Å² buried · 38 hydrogen bonds · protein-protein
E–H · 1505 Å² buried · 37 hydrogen bonds · protein-protein
F–G · 1480 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 1438 Å² buried · 37 hydrogen bonds · protein-protein
A–D · 503 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 25 modified (engineered).

Compared structures

3UHJ · Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021 · 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 Q92MR2
Elsewhere: RCSB PDB 3UHJ · PDBe 3UHJ · UniProt Q92MR2

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