MolNFT v1 · #159081 · protein
Crystal structure of GLUN2A agonist binding domain with 4-butyl-(S)- ccg-IV
6ODL · Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor…: “Crystal structure of GLUN2A agonist binding domain with 4-butyl-(S)- ccg-IV”. X-ray diffraction, 1 ligand (M7V), 4 pockets (best druggability 0.68). MolNFT v1 #159081 on…
- PDB
- 6ODL
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor ionotropic, NMDA 2A
- UniProt
- Q00959, G3V9C5
- Ligands
- M7V
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor ionotropic, NMDA 2A | protein | 278 | 32% helix, 26% strand | Q00959, G3V9C5 |
| B | Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor ionotropic, NMDA 2A | protein | 279 | 32% helix, 26% strand | Q00959, G3V9C5 |
Ligands and binding sites
- M7V · (1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.68 | 0.77 | 51 | empty |
| 2 | 725 | 0.68 | 0.76 | 86 | empty |
| 3 | 233 | 0.62 | 0.81 | 43 | M7V |
| 4 | 204 | 0.59 | 0.81 | 40 | M7V |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6ODL · Crystal structure of GluN2A agonist binding domain with 4-butyl-(S)-CCG-IV · 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 A 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 Q00959
- Every structure of UniProt G3V9C5
- Elsewhere: RCSB PDB 6ODL · PDBe 6ODL · UniProt Q00959 · UniProt G3V9C5
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