MolNFT v1 · #153489 · protein

GLUK3 receptor complex with UBP310

6JFZ · Glutamate receptor ionotropic, kainate 3: “GLUK3 receptor complex with UBP310”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #153489 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JFZ
Type: protein
Length: 2,869 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor ionotropic, kainate 3
UniProt: P42264
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 4 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor ionotropic, kainate 3	protein	718	42% helix, 16% strand	P42264
B	Glutamate receptor ionotropic, kainate 3	protein	714	42% helix, 15% strand	P42264
D	Glutamate receptor ionotropic, kainate 3	protein	719	43% helix, 17% strand	P42264
C	Glutamate receptor ionotropic, kainate 3	protein	718	43% helix, 16% strand	P42264

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	953	0.89	0.91	137	empty
2	1090	0.87	0.88	132	empty
3	651	0.86	0.90	99	empty
4	450	0.85	0.92	62	empty
5	629	0.85	0.89	90	empty

Interfaces

6 interfaces between chains.

D–C · 2314 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1989 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1595 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 1048 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 292 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6JFZ · GluK3 receptor complex with UBP310 · the same entry in another collection · chain C against C, TM-score 1.00
P42264 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 3 (P42264) · a predicted model of the same protein · chain A against A, TM-score 0.77

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 P42264
Elsewhere: RCSB PDB 6JFZ · PDBe 6JFZ · UniProt P42264

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