MolNFT v1 · #122683 · protein

Bacterial sodium channel pore domain, low bromide

5IWO · Ion transport protein: “Bacterial sodium channel pore domain, low bromide”. X-ray diffraction, 1 ligand (BR), 3 pockets (best druggability 0.78). MolNFT v1 #122683 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IWO
Type: protein
Length: 553 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ion transport protein
UniProt: Q0ABW0
Ligands: BR
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ion transport protein	protein	139	86% helix, 0% strand	Q0ABW0
B, C, D	Ion transport protein	protein	138	86% helix, 0% strand	Q0ABW0

Ligands and binding sites

BR · Bromide ion · ion · chains A, B, C, D

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	208	0.78	0.92	26	empty
2	675	0.78	0.82	63	empty
3	54	0.30	0.75	13	empty

Interfaces

6 interfaces between chains.

B–C · 1744 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1735 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 1726 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1679 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 133 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5IWO · Bacterial sodium channel pore domain, low bromide · the same entry in another collection · 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 Q0ABW0
Elsewhere: RCSB PDB 5IWO · PDBe 5IWO · UniProt Q0ABW0

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