MolNFT v1 · #141035 · protein

Crystal structure of voltage-gated sodium channel navab in high-pH condition

5YUA · Ion transport protein: “Crystal structure of voltage-gated sodium channel navab in high-pH condition”. X-ray diffraction, 3 ligands (PX4, 1N7, CA), 2 pockets (best druggability 0.47). MolNFT v1 #141035 on GenesisL1: 3D structure…

PDB: 5YUA
Type: protein
Length: 228 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ion transport protein
UniProt: A0A239WB15
Ligands: PX4, 1N7, CA
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ion transport protein	protein	228	83% helix, 0% strand	A0A239WB15

Ligands and binding sites

PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 6 copies · chains A
1N7 · Chapso · ligand · chains A
CA · Calcium ion · metal
LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.47	0.78	18	empty
2	89	0.34	0.74	18	empty

Compared structures

5YUA · Crystal structure of voltage-gated sodium channel NavAb in high-pH condition · 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 A0A239WB15
Elsewhere: RCSB PDB 5YUA · PDBe 5YUA · UniProt A0A239WB15

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