Research workbench

HBEST1 CA2+-bound partially open neck state

Analyse HBEST1 CA2+-bound partially open neck state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8D1K
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 0.76

Structure

electron microscopy · 1 distinct chain · 61% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B, A, E, C	Bestrophin-1	protein	376	61% helix, 1% strand	O76090

Ligands and binding sites

MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 40 copies · chains D, C, E, B, A
CA · Calcium ion · metal · 5 copies · chains D, C, B, A, 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	631	0.76	0.82	72	empty
2	180	0.68	0.87	30	empty
3	182	0.68	0.87	29	empty
4	158	0.66	0.87	25	empty
5	188	0.65	0.85	31	empty

Interfaces

10 interfaces between chains.

B–A · 5390 Å² buried · 56 hydrogen bonds · protein-protein
D–C · 5387 Å² buried · 56 hydrogen bonds · protein-protein
D–E · 5385 Å² buried · 56 hydrogen bonds · protein-protein
A–E · 5382 Å² buried · 56 hydrogen bonds · protein-protein
B–C · 5376 Å² buried · 56 hydrogen bonds · protein-protein

Compared structures

8D1K · hBest1 Ca2+-bound partially open neck state · the same entry in another collection · chain C against C, TM-score 1.00
O76090 · AlphaFold monomer V2.0 prediction for bestrophin-1 (O76090) · a predicted model of the same protein · chain A 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 8D1K · PDBe 8D1K · UniProt O76090

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