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

Analyse Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TPW
Type: protein
Length: 1,110 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: 10 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NMDA glutamate receptor subunit	protein	362	35% helix, 23% strand	Q91977
B	Glutamate receptor ionotropic, NMDA 2A	protein	331	30% helix, 20% strand	Q00959
H	Fab, heavy chain	protein	211	6% helix, 53% strand	—
L	Fab, light chain	protein	206	6% helix, 48% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
ZN · Zinc ion · metal · chains B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	971	0.75	0.78	120	SO4
2	89	0.74	0.97	28	empty
3	530	0.61	0.75	58	empty
4	231	0.58	0.79	35	empty
5	131	0.47	0.78	23	empty

Interfaces

5 interfaces between chains.

H–L · 1571 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1218 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 528 Å² buried · 17 hydrogen bonds · protein-protein
A–L · 246 Å² buried · 1 hydrogen bond · protein-protein
B–H · 146 Å² buried · 1 hydrogen bond · protein-protein

Modifications

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

Compared structures

5TPW · 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 0.95

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 5TPW · PDBe 5TPW · UniProt Q91977 · UniProt Q00959

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