MolNFT v1 · #54704 · protein

Crystal structure of 1-((2-fluoro-4-(3-(trifluoromethyl)-4,5,6,7- tetrahydro-1H-indazol-1-YL)PHENYL)METHYL)-2-pyrrolidinone in complex with the ligand binding domain of the rat GLUA2 receptor and glutamate at 2.2A resolution.

2XX9 · Glutamate receptor 2: “Crystal structure of 1-((2-fluoro-4-(3-(trifluoromethyl)-4,5,6,7…”. X-ray diffraction, 4 ligands (GLU, 1NF, ZN), 6 pockets (best druggability 0.81). MolNFT v1 #54704 on GenesisL1: 3D structure, binding sites…

PDB: 2XX9
Type: protein
Length: 784 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P19491
Ligands: GLU, 1NF, ZN, SO4
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glutamate receptor 2	protein	262	37% helix, 21% strand	P19491
C	Glutamate receptor 2	protein	260	38% helix, 21% strand	P19491

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
1NF · N,N-dimethyl-4-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]benzamide · ligand · 2 copies · chains A, C, B
ZN · Zinc ion · metal · 5 copies · chains A, B, C
SO4 · Sulfate ion · ion · 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	666	0.81	0.86	92	1NF
2	366	0.67	0.81	39	empty
3	262	0.57	0.78	30	empty
4	108	0.41	0.77	23	empty
5	65	0.37	0.78	20	empty

Interfaces

3 interfaces between chains.

A–C · 837 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 266 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 46 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

2XX9 · Crystal structure of 1-((2-fluoro-4-(3-(trifluoromethyl)-4,5,6,7… · the same entry in another collection · chain A against A, TM-score 1.00
P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · 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 P19491
Elsewhere: RCSB PDB 2XX9 · PDBe 2XX9 · UniProt P19491

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