MolNFT v1 · #135139 · protein

Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2A in complex with zinc at GLUN1 and GLUN2A

5TQ2 · NMDA glutamate receptor subunit: “Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2A in complex with…”. X-ray diffraction, 3 ligands (NAG, ZN, SO4), 15 pockets (best druggability 0.72). MolNFT…

PDB: 5TQ2
Type: protein
Length: 1,107 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NMDA glutamate receptor subunit; Glutamate receptor ionotropic, NMDA 2A; Fab, heavy…
UniProt: Q91977, Q00959
Ligands: NAG, ZN, SO4
Pockets: 15 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 23% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NMDA glutamate receptor subunit	protein	365	35% helix, 22% strand	Q91977
B	Glutamate receptor ionotropic, NMDA 2A	protein	335	32% helix, 19% strand	Q00959
H	Fab, heavy chain	protein	205	6% helix, 41% strand	—
L	Fab, light chain	protein	202	3% helix, 47% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
ZN · Zinc ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, H, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	651	0.72	0.79	89	empty
2	69	0.67	0.94	20	empty
3	552	0.65	0.76	55	empty
4	201	0.54	0.78	35	empty
5	162	0.53	0.79	31	empty

Interfaces

5 interfaces between chains.

H–L · 1492 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1299 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 430 Å² buried · 22 hydrogen bonds · protein-protein
A–L · 196 Å² buried · 4 hydrogen bonds · protein-protein
B–H · 135 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5TQ2 · Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A… · 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 0.96

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 Q91977
Every structure of UniProt Q00959
Elsewhere: RCSB PDB 5TQ2 · PDBe 5TQ2 · UniProt Q91977 · UniProt Q00959

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