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AGME bound to ADP-B-mannose

Analyse AGME bound to ADP-B-mannose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X6T
Type: protein
Length: 3,071 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.36
Source: ESCHERICHIA COLI
Molecule: ADP-L-glycero-D-manno-heptose-6-epimerase
EC: 5.1.3.20
UniProt: P67911
Ligands: NAP, ADP, BMA, CL
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · resolution 2.36 · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, H, I, J	ADP-L-glycero-D-manno-heptose-6-epimerase (EC 5.1.3.20)	protein	307	45% helix, 17% strand	P67911
G	ADP-L-glycero-D-manno-heptose-6-epimerase (EC 5.1.3.20)	protein	308	45% helix, 17% strand	P67911

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
BMA · beta-D-mannopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
CL · Chloride ion · ion · 2 copies · chains G
GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	745	0.84	0.87	71	NAP, ADP, BMA
2	740	0.83	0.86	72	NAP, ADP, BMA
3	767	0.83	0.86	74	NAP, ADP, BMA
4	761	0.83	0.86	69	NAP, ADP, BMA
5	763	0.83	0.86	71	NAP, ADP, BMA

Interfaces

12 interfaces between chains.

G–H · 836 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 829 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 828 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 825 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 824 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2X6T · Agme bound to ADP-B-mannose · the same entry in another collection · chain J against J, TM-score 1.00
P67911 · AlphaFold monomer V2.0 prediction for ADP-L-glycero-D-manno- heptose-6-epimerase (P67911) · a predicted model of the same protein · chain G 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 P67911
Elsewhere: RCSB PDB 2X6T · PDBe 2X6T · UniProt P67911

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