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Cryo-EM structure of calcium-bound MTMEM16F lipid scramblase in digitonin

Analyse Cryo-EM structure of calcium-bound MTMEM16F lipid scramblase in digitonin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QP6
Type: protein
Length: 1,482 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anoctamin-6
UniProt: Q6P9J9
Ligands: P1O, CA
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 58% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Anoctamin-6	protein	741	58% helix, 6% strand	Q6P9J9

Ligands and binding sites

P1O · 1,2-didecanoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 6 copies · chains 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	924	0.81	0.83	64	empty
2	1028	0.80	0.81	65	empty
3	293	0.72	0.85	43	P1O
4	309	0.72	0.85	48	P1O
5	174	0.71	0.89	34	empty

Interfaces

1 interface between chains.

A–B · 947 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6QP6 · Cryo-EM structure of calcium-bound mTMEM16F lipid scramblase in digitonin · the same entry in another collection · chain A against A, TM-score 1.00
Q6P9J9 · AlphaFold monomer V2.0 prediction for anoctamin-6 (Q6P9J9) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q6P9J9
Elsewhere: RCSB PDB 6QP6 · PDBe 6QP6 · UniProt Q6P9J9

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