MolNFT v1 · #167858 · protein

Nachbac-NAV1.7VSDII chimera in nanodisc

6VXO: “Nachbac-NAV1.7VSDII chimera in nanodisc”. Electron microscopy, 1 ligand (POV), 20 pockets (best druggability 0.82). MolNFT v1 #167858 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VXO
Type: protein
Length: 904 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nachbac-NAV1.7VSDII chimera
UniProt: Q9KCR8, Q15858
Ligands: POV
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E	Nachbac-NAV1.7VSDII chimera	protein	226	65% helix, 0% strand	Q9KCR8, Q15858

Ligands and binding sites

POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 12 copies · chains A, 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	618	0.82	0.86	49	empty
2	222	0.63	0.82	29	empty
3	249	0.62	0.81	29	empty
4	260	0.61	0.80	30	empty
5	385	0.61	0.75	31	POV

Interfaces

6 interfaces between chains.

A–E · 1659 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 1646 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 1644 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 1642 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 20 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6VXO · NaChBac-Nav1.7VSDII chimera in nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
Q15858 · AlphaFold monomer V2.0 prediction for sodium channel protein type 9 subunit alpha (Q15858) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 Q9KCR8
Every structure of UniProt Q15858
Elsewhere: RCSB PDB 6VXO · PDBe 6VXO · UniProt Q9KCR8 · UniProt Q15858

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