MolNFT v1 · #122625 · protein

Glic-V135C bimane labelled X-ray structure

5IUX · Proton-gated ion channel: “Glic-V135C bimane labelled X-ray structure”. X-ray diffraction, 4 ligands (PC1, 6E3, NA), 20 pockets (best druggability 0.82). MolNFT v1 #122625 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5IUX
Type: protein
Length: 1,555 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proton-gated ion channel
UniProt: Q7NDN8
Ligands: PC1, 6E3, NA, BR
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 34% strand (DSSP).

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

Ligands and binding sites

PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 15 copies · chains A, E, B, C, D
6E3 · 2,3,5,6-tetramethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione · ligand · 2 copies · chains A, E, C, D
NA · Sodium ion · metal · 4 copies · chains B, C, D, E
BR · Bromide ion · ion · 5 copies · chains A, B, C, D, E
ACT · Acetate ion · additive · 10 copies · chains A, E, B, C, D
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	1116	0.82	0.82	62	LMT
2	402	0.72	0.83	50	empty
3	381	0.72	0.83	45	empty
4	653	0.72	0.79	64	BR, NA, ACT
5	365	0.71	0.83	45	empty

Interfaces

5 interfaces between chains.

C–D · 2312 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 2305 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 2280 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 2242 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 2213 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5IUX · GLIC-V135C bimane labelled X-ray structure · 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 5IUX · PDBe 5IUX · UniProt Q7NDN8

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