MolNFT v1 · #167844 · protein

Bestrophin-2 CA2+-bound state (250 nm CA2+)

6VX6: “Bestrophin-2 CA2+-bound state (250 nm CA2+)”. Electron microscopy, 2 ligands (CA, CL), 20 pockets (best druggability 0.79). MolNFT v1 #167844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VX6
Type: protein
Length: 1,830 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bestrophin
UniProt: E1BF86
Ligands: CA, CL
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 62% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, A, B, C, D	Bestrophin	protein	366	62% helix, 1% strand	E1BF86

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains E, D, A, B, C
CL · Chloride ion · ion · chains E, A, B, 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	922	0.79	0.81	58	empty
2	1125	0.76	0.79	132	CL
3	819	0.66	0.74	81	empty
4	347	0.62	0.78	45	empty
5	328	0.62	0.78	39	empty

Interfaces

10 interfaces between chains.

E–A · 5397 Å² buried · 45 hydrogen bonds · protein-protein
C–D · 5383 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 5383 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 5378 Å² buried · 35 hydrogen bonds · protein-protein
E–D · 5343 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

6VX6 · bestrophin-2 Ca2+-bound state (250 nM Ca2+) · the same entry in another collection · chain E against E, 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 E1BF86
Elsewhere: RCSB PDB 6VX6 · PDBe 6VX6 · UniProt E1BF86

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