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Crystal structure of glic with mutations at the loop C region

Analyse Crystal structure of glic with mutations at the loop C region in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IRE
Type: protein
Length: 1,561 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proton-gated ion channel
UniProt: Q7NDN8
Ligands: OXL, PC1, LMD
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proton-gated ion channel	protein	312	35% helix, 34% strand	Q7NDN8
B, D	Proton-gated ion channel	protein	313	35% helix, 34% strand	Q7NDN8
C	Proton-gated ion channel	protein	311	36% helix, 34% strand	Q7NDN8
E	Proton-gated ion channel	protein	312	37% helix, 34% strand	Q7NDN8

Ligands and binding sites

OXL · Oxalate ion · ligand · 17 copies · chains A, B, E, C, D
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 10 copies · chains A, E, B, C, D
LMD · tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 6 copies · chains A, B, E, C, D
ACT · Acetate ion · additive · 10 copies · chains A, E, B, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1118	0.80	0.81	60	LMD
2	86	0.76	0.97	20	empty
3	407	0.75	0.85	49	empty
4	431	0.74	0.84	51	empty
5	381	0.73	0.84	53	empty

Interfaces

6 interfaces between chains.

A–B · 2297 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 2228 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 2227 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 2222 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 2219 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4IRE · Crystal structure of GLIC with mutations at the loop C region · 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 D 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 4IRE · PDBe 4IRE · UniProt Q7NDN8

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