MolNFT v1 · #78489 · protein

Crystal structure of glutamate receptor GLUA1 amino terminal domain

3SAJ · Glutamate receptor 1: “Crystal structure of glutamate receptor GLUA1 amino terminal domain”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.82). MolNFT v1 #78489 on GenesisL1: 3D structure, binding…

PDB: 3SAJ
Type: protein
Length: 1,474 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 1
UniProt: P19490
Ligands: NAG, BMA, MAN
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor 1	protein	369	37% helix, 23% strand	P19490
B	Glutamate receptor 1	protein	366	37% helix, 23% strand	P19490
C	Glutamate receptor 1	protein	372	35% helix, 23% strand	P19490
D	Glutamate receptor 1	protein	367	39% helix, 23% strand	P19490

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, C, B, D
BMA · beta-D-mannopyranose · sugar · 4 copies
MAN · alpha-D-mannopyranose · sugar · 4 copies

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1075	0.82	0.83	115	empty
2	1014	0.81	0.82	98	empty
3	642	0.74	0.81	61	empty
4	78	0.69	0.94	21	empty
5	165	0.68	0.88	29	empty

Interfaces

5 interfaces between chains.

A–C · 1724 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1409 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 886 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 780 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 555 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 glycan, 3 disulfide (N-glycosylation, disulfide, glycosylation).

Compared structures

3SAJ · Crystal Structure of glutamate receptor GluA1 Amino Terminal Domain · the same entry in another collection · chain D against D, TM-score 1.00
P19490 · AlphaFold monomer V2.0 prediction for glutamate receptor 1 (P19490) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P19490
Elsewhere: RCSB PDB 3SAJ · PDBe 3SAJ · UniProt P19490

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