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Xray structure of GLIC in complex with fumarate

Analyse Xray structure of GLIC in complex with fumarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HJ3
Type: protein
Length: 1,555 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.7
Source: Gloeobacter violaceus
Molecule: Proton-gated ion channel
UniProt: Q7NDN8
Ligands: PLC, FUM, NA, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.7 · 1 distinct chain · 38% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	38% helix, 34% strand	Q7NDN8

Ligands and binding sites

PLC · Diundecyl phosphatidyl choline · ligand · 15 copies · chains A, B, E, C, D
FUM · Fumaric acid · ligand · 5 copies · chains A, E, B, C, D
NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E
LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, E, C, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1144	0.81	0.82	62	LMT, NA
2	368	0.73	0.84	49	empty
3	370	0.71	0.83	48	empty
4	388	0.71	0.83	48	empty
5	388	0.71	0.82	50	empty

Interfaces

5 interfaces between chains.

A–B · 2342 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2320 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 2317 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 2309 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 2283 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6HJ3 · Xray structure of glic in complex with fumarate · the same entry in another collection · chain E against E, TM-score 1.00
Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · 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 Q7NDN8
Elsewhere: RCSB PDB 6HJ3 · PDBe 6HJ3 · UniProt Q7NDN8

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