MolNFT v1 · #191294 · protein

HBEST2 1UM CA2+ (CA2+-bound) closed state

8D1E · Bestrophin-2: “HBEST2 1UM CA2+ (CA2+-bound) closed state”. Electron microscopy, 4 ligands (MC3, DU0, CA), 20 pockets (best druggability 0.76). MolNFT v1 #191294 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8D1E
Type: protein
Length: 1,880 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 0.76

Structure

electron microscopy · 1 distinct chain · 64% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, C, A, B	Bestrophin-2	protein	376	64% helix, 1% strand	Q8NFU1

Ligands and binding sites

MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 50 copies · chains D, C, E, A, 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 D, E, C, A, B
CA · Calcium ion · metal · 5 copies · chains D, C, E, B, A
CL · Chloride ion · ion · chains D, E, C, A, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	842	0.76	0.79	74	empty
2	485	0.69	0.80	55	empty
3	497	0.69	0.79	56	empty
4	50	0.69	0.97	15	empty
5	194	0.64	0.84	32	empty

Interfaces

10 interfaces between chains.

A–B · 5478 Å² buried · 52 hydrogen bonds · protein-protein
D–C · 5473 Å² buried · 52 hydrogen bonds · protein-protein
D–E · 5471 Å² buried · 52 hydrogen bonds · protein-protein
E–A · 5469 Å² buried · 52 hydrogen bonds · protein-protein
C–B · 5463 Å² buried · 52 hydrogen bonds · protein-protein

Compared structures

8D1E · hBest2 1uM Ca2+ (Ca2+-bound) closed state · the same entry in another collection · chain B against B, TM-score 1.00
Q8NFU1 · AlphaFold monomer V2.0 prediction for bestrophin-2 (Q8NFU1) · a predicted model of the same protein · chain C 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 8D1E · PDBe 8D1E · UniProt Q8NFU1

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