MolNFT v1 · #191304 · protein

HBEST1_345 CA2+-bound open state

8D1O · Bestrophin-1: “HBEST1_345 CA2+-bound open state”. Electron microscopy, 2 ligands (MC3, CA), 20 pockets (best druggability 0.73). MolNFT v1 #191304 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8D1O
Type: protein
Length: 1,690 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 0.73

Structure

electron microscopy · 1 distinct chain · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, A, B, C, D	Bestrophin-1	protein	338	67% helix, 0% strand	O76090

Ligands and binding sites

MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 40 copies · chains E, A, D, B, C
CA · Calcium ion · metal · 5 copies · 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	694	0.73	0.79	130	empty
2	972	0.69	0.74	74	empty
3	587	0.67	0.77	56	empty
4	136	0.67	0.88	26	empty
5	132	0.66	0.88	25	empty

Interfaces

10 interfaces between chains.

E–A · 4386 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 4385 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 4377 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 4373 Å² buried · 42 hydrogen bonds · protein-protein
E–D · 4365 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

8D1O · hBest1_345 Ca2+-bound open state · the same entry in another collection · chain D against D, 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 8D1O · PDBe 8D1O · UniProt O76090

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