MolNFT v2 · #152481 · protein

X-ray structure of GLIC in complex with propionate

6HPP · Proton-gated ion channel: “X-ray structure of GLIC in complex with propionate”. X-ray diffraction at 3.2, 2 ligands (NA, CL), 20 pockets (best druggability 0.80). MolNFT v2 #152481 on GenesisL1: 3D structure, binding sites and…

PDB: 6HPP
Type: protein
Length: 1,555 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Gloeobacter violaceus (strain PCC 7421)
Molecule: Proton-gated ion channel
UniProt: Q7NDN8
Ligands: NA, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · resolution 3.2 · 1 distinct chain · 36% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	36% helix, 32% strand	Q7NDN8

Ligands and binding sites

NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E
PPI · Propanoic acid · additive · 10 copies · chains A, B, E, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1166	0.80	0.81	58	NA, LMT
2	405	0.71	0.82	48	empty
3	379	0.71	0.83	51	empty
4	354	0.71	0.83	46	empty
5	369	0.70	0.82	49	empty

Interfaces

5 interfaces between chains.

B–C · 2311 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 2287 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 2266 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 2253 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 2224 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6HPP · X-ray structure of glic in complex with propionate · 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 6HPP · PDBe 6HPP · UniProt Q7NDN8

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