MolNFT v1 · #136881 · protein

Crystal structure of the highly open channel-stabilized mutant C27S + K33C + I9'A + N21'C of glic under reducing conditions.

5V6N · Proton-gated ion channel: “Crystal structure of the highly open channel-stabilized mutant C27S + K33C + I9'A + N21'C of glic under…”. X-ray diffraction, 2 ligands (NA, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #136881 on…

PDB: 5V6N
Type: protein
Length: 1,550 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proton-gated ion channel
UniProt: Q7NDN8
Ligands: NA, SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A, B, D, E	Proton-gated ion channel	protein	310	35% helix, 35% strand	Q7NDN8

Ligands and binding sites

NA · Sodium ion · metal · chains C, A, B, D, E
SO4 · Sulfate ion · ion · 5 copies · chains A, E, C, B, D
LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains C, B, D, A, E

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1041	0.81	0.81	81	LMT, NA
2	515	0.76	0.84	61	empty
3	516	0.74	0.82	61	empty
4	496	0.74	0.82	54	empty
5	87	0.74	0.96	20	empty

Interfaces

5 interfaces between chains.

D–E · 2246 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 2185 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 2177 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 2146 Å² buried · 10 hydrogen bonds · protein-protein
C–B · 2128 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5V6N · Crystal Structure of the highly open channel-stabilized mutant C27S + K33C + I9'A + N21'C… · 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 C against A, TM-score 0.99

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 5V6N · PDBe 5V6N · UniProt Q7NDN8

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