MolNFT v1 · #50236 · protein

Crystal structure of the NR3B ligand binding core complex with D- serine at 1.62 ångström resolution

2RCB · Glutamate [NMDA] receptor subunit 3B: “Crystal structure of the NR3B ligand binding core complex with D- serine at 1.62 ångström resolution”. X-ray diffraction, 1 ligand (DSN), 2 pockets (best druggability 0.78). MolNFT v1 #50236 on…

PDB: 2RCB
Type: protein
Length: 564 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate [NMDA] receptor subunit 3B
UniProt: Q8VHN2
Ligands: DSN
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glutamate [NMDA] receptor subunit 3B	protein	282	36% helix, 26% strand	Q8VHN2

Ligands and binding sites

DSN · D-serine · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.78	0.80	115	empty
2	181	0.60	0.83	31	empty

Interfaces

1 interface between chains.

A–B · 861 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2RCB · Crystal structure of the NR3B ligand binding core complex with D-serine at 1.62 Angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
Q8VHN2 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 3B (Q8VHN2) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q8VHN2
Elsewhere: RCSB PDB 2RCB · PDBe 2RCB · UniProt Q8VHN2

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