Research workbench

HBEST2 CA2+-bound open state

Analyse HBEST2 CA2+-bound open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8D1G
Type: protein
Length: 1,735 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bestrophin-2
UniProt: Q8NFU1
Ligands: MC3, DU0, CA, CL
Pockets: 20 · best druggability 0.71

Structure

electron microscopy · 1 distinct chain · 68% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, C, D	Bestrophin-2	protein	347	68% helix, 1% strand	Q8NFU1

Ligands and binding sites

MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 50 copies · chains A, B, E, C, D
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 A, B, E, C, D
CA · Calcium ion · metal · 5 copies · chains A, E, B, D, C
CL · Chloride ion · ion · chains A, B, E, 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	974	0.71	0.75	82	empty
2	221	0.71	0.87	45	empty
3	183	0.71	0.88	41	empty
4	203	0.71	0.87	46	empty
5	202	0.70	0.87	42	empty

Interfaces

10 interfaces between chains.

A–E · 4748 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 4740 Å² buried · 37 hydrogen bonds · protein-protein
E–D · 4738 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 4736 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 4729 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

8D1G · hBest2 Ca2+-bound open state · the same entry in another collection · chain D against D, TM-score 1.00
Q8NFU1 · AlphaFold monomer V2.0 prediction for bestrophin-2 (Q8NFU1) · a predicted model of the same protein · chain B 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 Q8NFU1
Elsewhere: RCSB PDB 8D1G · PDBe 8D1G · UniProt Q8NFU1

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