MolNFT v1 · #119485 · protein

GLUN1B-GLUN2B NMDA receptor structure-class Y

5FXK · N-methyl-D-aspartate receptor GLUN1: “GLUN1B-GLUN2B NMDA receptor structure-class Y”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #119485 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FXK
Type: protein
Length: 3,118 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-methyl-D-aspartate receptor GLUN1; N-methyl-D-aspartate receptor GLUN2B
UniProt: P35439, Q00960
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 4 distinct chains · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-methyl-D-aspartate receptor GLUN1	protein	793	39% helix, 13% strand	P35439
B	N-methyl-D-aspartate receptor GLUN2B	protein	767	38% helix, 14% strand	Q00960
C	N-methyl-D-aspartate receptor GLUN1	protein	792	39% helix, 13% strand	P35439
D	N-methyl-D-aspartate receptor GLUN2B	protein	766	38% helix, 14% strand	Q00960

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	839	0.85	0.88	149	empty
2	906	0.82	0.84	145	empty
3	601	0.81	0.87	102	empty
4	526	0.80	0.86	98	empty
5	688	0.79	0.84	101	empty

Interfaces

4 interfaces between chains.

A–B · 1279 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 1271 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 865 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 855 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5FXK · GluN1b-GluN2B NMDA receptor structure-Class Y · the same entry in another collection · chain D against D, TM-score 1.00
Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain B against A, TM-score 0.92
P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain C against A, TM-score 0.90

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 P35439
Every structure of UniProt Q00960
Elsewhere: RCSB PDB 5FXK · PDBe 5FXK · UniProt P35439 · UniProt Q00960

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.