MolNFT v1 · #191303 · protein

BBEST2_345 CA2+-bound open state

8D1N · Bestrophin: “BBEST2_345 CA2+-bound open state”. Electron microscopy, 4 ligands (MC3, DU0, CA), 20 pockets (best druggability 0.74). MolNFT v1 #191303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8D1N
Type: protein
Length: 1,690 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bestrophin
UniProt: E1BF86
Ligands: MC3, DU0, CA, CL
Pockets: 20 · best druggability 0.74

Structure

electron microscopy · 1 distinct chain · 70% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, D, A, C, B	Bestrophin	protein	338	70% helix, 1% strand	E1BF86

Ligands and binding sites

MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 50 copies · chains E, A, D, C, B
DU0 · 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R}, 9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4, 8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol · ligand · 5 copies · chains E, D, A, C, B
CA · Calcium ion · metal · 5 copies · chains E, D, C, A, B
CL · Chloride ion · ion · chains E, D, A, C, B

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	779	0.74	0.79	104	CL
2	862	0.73	0.77	81	empty
3	179	0.62	0.83	27	empty
4	262	0.60	0.79	45	empty
5	173	0.59	0.82	25	empty

Interfaces

5 interfaces between chains.

C–B · 4477 Å² buried · 39 hydrogen bonds · protein-protein
E–A · 4475 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 4471 Å² buried · 39 hydrogen bonds · protein-protein
E–D · 4469 Å² buried · 39 hydrogen bonds · protein-protein
D–C · 4462 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

8D1N · bBest2_345 Ca2+-bound open state · 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 8D1N · PDBe 8D1N · UniProt E1BF86

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.