MolNFT v1 · #191299 · protein

HBEST1 5MM CA2+ (CA2+-bound) closed state

8D1J · Bestrophin-1: “HBEST1 5MM CA2+ (CA2+-bound) closed state”. Electron microscopy, 2 ligands (MC3, CA), 20 pockets (best druggability 0.78). MolNFT v1 #191299 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8D1J
Type: protein
Length: 1,880 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bestrophin-1
UniProt: O76090
Ligands: MC3, CA
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 1 distinct chain · 63% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, B, D, E	Bestrophin-1	protein	376	63% helix, 1% strand	O76090

Ligands and binding sites

MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 40 copies · chains A, B, E, C, D
CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.78	0.97	15	empty
2	105	0.78	0.97	16	empty
3	102	0.77	0.97	15	empty
4	100	0.76	0.96	15	empty
5	100	0.76	0.96	17	empty

Interfaces

10 interfaces between chains.

A–B · 5413 Å² buried · 54 hydrogen bonds · protein-protein
A–E · 5412 Å² buried · 54 hydrogen bonds · protein-protein
D–E · 5398 Å² buried · 54 hydrogen bonds · protein-protein
C–D · 5391 Å² buried · 54 hydrogen bonds · protein-protein
C–B · 5383 Å² buried · 54 hydrogen bonds · protein-protein

Compared structures

8D1J · hBest1 5mM Ca2+ (Ca2+-bound) closed state · the same entry in another collection · chain E against E, TM-score 1.00
O76090 · AlphaFold monomer V2.0 prediction for bestrophin-1 (O76090) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 O76090
Elsewhere: RCSB PDB 8D1J · PDBe 8D1J · UniProt O76090

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