MolNFT v1 · #143400 · protein

TRPML3/ML-SA1 complex at pH 7.4

6AYF · Mucolipin-3: “TRPML3/ML-SA1 complex at pH 7.4”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #143400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6AYF
Type: protein
Length: 1,904 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucolipin-3
UniProt: Q8TDD5
Ligands: NAG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 58% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Mucolipin-3	protein	476	58% helix, 15% strand	Q8TDD5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, D, B, C

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	1145	0.86	0.86	55	empty
2	853	0.73	0.77	56	empty
3	863	0.73	0.77	56	empty
4	815	0.73	0.77	57	empty
5	840	0.72	0.77	56	empty

Interfaces

4 interfaces between chains.

C–D · 3742 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 3731 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 3725 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 3720 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan (N-glycosylation).

Compared structures

6AYF · TRPML3/ML-SA1 complex at pH 7.4 · the same entry in another collection · chain A against A, TM-score 1.00
Q8TDD5 · AlphaFold monomer V2.0 prediction for mucolipin-3 (Q8TDD5) · 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 Q8TDD5
Elsewhere: RCSB PDB 6AYF · PDBe 6AYF · UniProt Q8TDD5

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