MolNFT v1 · #161793 · protein

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

6QPC · Anoctamin-6: “Cryo-EM structure of calcium-bound MTMEM16F lipid scramblase in nanodisc”. Electron microscopy, 2 ligands (P1O, CA), 20 pockets (best druggability 0.76). MolNFT v1 #161793 on GenesisL1: 3D structure, binding sites and…

PDB: 6QPC
Type: protein
Length: 1,154 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 0.76

Structure

electron microscopy · 1 distinct chain · 65% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Anoctamin-6	protein	577	65% helix, 2% strand	Q6P9J9

Ligands and binding sites

P1O · 1,2-didecanoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 4 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	249	0.76	0.89	36	P1O
2	298	0.74	0.86	43	P1O
3	541	0.67	0.77	52	empty
4	274	0.65	0.82	31	empty
5	460	0.65	0.77	61	empty

Interfaces

1 interface between chains.

A–B · 725 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

6QPC · Cryo-EM structure of calcium-bound mTMEM16F lipid scramblase in nanodisc · 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 0.95

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 6QPC · PDBe 6QPC · UniProt Q6P9J9

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