MolNFT v1 · #152724 · protein

Structure of the human GLUN1/GLUN2A NMDA receptor in the GLUTAMATE/GLYCINE-bound state at pH 7.8

6IRA · Glutamate receptor ionotropic, NMDA 2A: “Structure of the human GLUN1/GLUN2A NMDA receptor in the GLUTAMATE/GLYCINE-bound state at pH 7.8”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #152724 on GenesisL1: 3D…

PDB: 6IRA
Type: protein
Length: 3,080 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor ionotropic, NMDA 2A; Glutamate receptor ionotropic, NMDA 1
UniProt: Q12879, Q05586
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B	Glutamate receptor ionotropic, NMDA 2A	protein	751	37% helix, 16% strand	Q12879
A, C	Glutamate receptor ionotropic, NMDA 1	protein	789	38% helix, 17% strand	Q05586

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	1038	0.85	0.86	137	empty
2	1084	0.84	0.85	131	empty
3	610	0.84	0.88	66	empty
4	1102	0.83	0.84	135	empty
5	752	0.79	0.83	72	empty

Interfaces

5 interfaces between chains.

D–C · 3416 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 3357 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 2713 Å² buried · 14 hydrogen bonds · protein-protein
D–A · 2695 Å² buried · 11 hydrogen bonds · protein-protein
D–B · 273 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6IRA · Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at… · the same entry in another collection · chain D against D, TM-score 1.00
Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain A against A, TM-score 0.97
Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain D against A, TM-score 0.91

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 Q12879
Every structure of UniProt Q05586
Elsewhere: RCSB PDB 6IRA · PDBe 6IRA · UniProt Q12879 · UniProt Q05586

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