MolNFT v1 · #30660 · protein

Crystal structure of the NR1/NR2A ligand-binding cores complex

2A5T · N-methyl-D-aspartate receptor NMDAR1-4A subunit: “Crystal structure of the NR1/NR2A ligand-binding cores complex”. X-ray diffraction, 2 ligands (GLY, GLU), 6 pockets (best druggability 0.77). MolNFT v1 #30660 on GenesisL1: 3D…

PDB: 2A5T
Type: protein
Length: 547 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-methyl-D-aspartate receptor NMDAR1-4A subunit; N-methyl-D-aspartate receptor NMDAR2A…
UniProt: P35439, Q00959
Ligands: GLY, GLU
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-methyl-D-aspartate receptor NMDAR1-4A subunit	protein	271	32% helix, 28% strand	P35439
B	N-methyl-D-aspartate receptor NMDAR2A subunit	protein	276	33% helix, 27% strand	Q00959

Ligands and binding sites

GLY · Glycine · ligand · chains A
GLU · Glutamic acid · ligand · chains 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	691	0.77	0.82	73	empty
2	82	0.57	0.87	28	empty
3	232	0.55	0.78	37	empty
4	133	0.46	0.77	29	empty
5	82	0.33	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 1032 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2A5T · Crystal Structure Of The NR1/NR2A ligand-binding cores complex · 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 2A5T · PDBe 2A5T · UniProt P35439 · UniProt Q00959

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