MolNFT v1 · #121770 · protein

Glutamate- and glycine-bound GLUN1/GLUN2A agonist binding domains with mpx-004

5I58 · Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor…: “Glutamate- and glycine-bound GLUN1/GLUN2A agonist binding domains with mpx-004”. X-ray diffraction, 3 ligands (GLY, GLU, 67R), 6 pockets (best druggability 0.78). MolNFT v1…

PDB: 5I58
Type: protein
Length: 534 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor ionotropic, NMDA 1; Glutamate…
UniProt: P35439, Q00959
Ligands: GLY, GLU, 67R
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor ionotropic, NMDA 1	protein	257	33% helix, 26% strand	P35439
B	Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor ionotropic, NMDA 2A	protein	277	33% helix, 25% strand	Q00959

Ligands and binding sites

GLY · Glycine · ligand · chains A
GLU · Glutamic acid · ligand · chains B
67R · 5-({[(3-chloro-4-fluorophenyl)sulfonyl]amino}methyl)-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide · ligand · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.78	0.84	80	67R
2	247	0.56	0.78	25	empty
3	95	0.55	0.85	22	empty
4	115	0.37	0.74	21	empty
5	63	0.35	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 1120 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5I58 · Glutamate- and glycine-bound GLUN1/GLUN2A agonist binding domains with mpx-004 · the same entry in another collection · chain A against A, TM-score 1.00
Q00959 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q00959) · a predicted model of the same protein · chain B against A, TM-score 0.98
P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q00959
Elsewhere: RCSB PDB 5I58 · PDBe 5I58 · UniProt P35439 · UniProt Q00959

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