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Bacteroides salyersiae GH164 beta-mannosidase in complex with mannoimidazole

Analyse Bacteroides salyersiae GH164 beta-mannosidase in complex with mannoimidazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T7G
Type: protein
Length: 3,927 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.8
Source: Bacteroides salyersiae CL02T12C01
Molecule: Glyco_hydro_42M domain-containing protein
UniProt: I9SUA3
Ligands: MVL, CL
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · resolution 1.8 · 6 distinct chains · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
AAA	Glyco_hydro_42M domain-containing protein	protein	661	34% helix, 24% strand	I9SUA3
DDD	Glyco_hydro_42M domain-containing protein	protein	658	33% helix, 24% strand	I9SUA3
CCC	Glyco_hydro_42M domain-containing protein	protein	654	33% helix, 25% strand	I9SUA3
BBB	Glyco_hydro_42M domain-containing protein	protein	652	34% helix, 25% strand	I9SUA3
FFF	Glyco_hydro_42M domain-containing protein	protein	654	33% helix, 25% strand	I9SUA3
EEE	Glyco_hydro_42M domain-containing protein	protein	648	34% helix, 25% strand	I9SUA3

Ligands and binding sites

MVL · (5R,6R,7S,8R)-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol · ligand · 6 copies · chains AAA, DDD, CCC, BBB, FFF, EEE
CL · Chloride ion · ion · 6 copies · chains AAA, DDD, CCC, BBB, FFF, EEE
EDO · 1,2-ethanediol · additive · 16 copies · chains AAA, DDD, CCC, BBB, FFF, EEE

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.71	0.97	29	empty
2	921	0.70	0.75	96	empty
3	70	0.69	0.95	30	empty
4	620	0.68	0.77	57	EDO
5	478	0.68	0.79	64	MVL, EDO

Interfaces

9 interfaces between chains.

DDD–FFF · 1453 Å² buried · 22 hydrogen bonds · protein-protein
FFF–EEE · 1442 Å² buried · 23 hydrogen bonds · protein-protein
CCC–BBB · 1441 Å² buried · 22 hydrogen bonds · protein-protein
DDD–EEE · 1430 Å² buried · 20 hydrogen bonds · protein-protein
AAA–CCC · 1426 Å² buried · 20 hydrogen bonds · protein-protein

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 I9SUA3
Elsewhere: RCSB PDB 6T7G · PDBe 6T7G · UniProt I9SUA3

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