MolNFT v1 · #151573 · protein

Structure of the TRPML2 eld at pH 4.5

6HRS · Mucolipin-2: “Structure of the TRPML2 eld at pH 4.5”. X-ray diffraction, 17 pockets (best druggability 0.65). MolNFT v1 #151573 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HRS
Type: protein
Length: 1,491 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucolipin-2
UniProt: Q8IZK6
Pockets: 17 · best druggability 0.65

Structure

x-ray diffraction · 8 distinct chains · 27% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mucolipin-2	protein	185	26% helix, 32% strand	Q8IZK6
B	Mucolipin-2	protein	191	28% helix, 31% strand	Q8IZK6
C	Mucolipin-2	protein	187	27% helix, 32% strand	Q8IZK6
D	Mucolipin-2	protein	189	28% helix, 36% strand	Q8IZK6
E	Mucolipin-2	protein	187	28% helix, 33% strand	Q8IZK6
F	Mucolipin-2	protein	182	25% helix, 33% strand	Q8IZK6
G	Mucolipin-2	protein	187	26% helix, 35% strand	Q8IZK6
H	Mucolipin-2	protein	183	29% helix, 36% strand	Q8IZK6

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.65	0.90	21	empty
2	152	0.64	0.86	31	empty
3	279	0.61	0.79	41	empty
4	157	0.58	0.82	29	empty
5	131	0.52	0.80	24	empty

Interfaces

9 interfaces between chains.

B–D · 1215 Å² buried · 8 hydrogen bonds · protein-protein
E–G · 1064 Å² buried · 12 hydrogen bonds · protein-protein
F–H · 1008 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 984 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 968 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6HRS · Structure of the TRPML2 ELD at pH 4.5 · the same entry in another collection · chain H against H, TM-score 1.00
Q8IZK6 · AlphaFold monomer V2.0 prediction for mucolipin-2 (Q8IZK6) · a predicted model of the same protein · chain H against A, TM-score 0.93

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 Q8IZK6
Elsewhere: RCSB PDB 6HRS · PDBe 6HRS · UniProt Q8IZK6

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