MolNFT v1 · #124324 · protein
Cryo-EM structure of GLUA2 bound to antagonist ZK200775 at 6.8 ångström resolution
5KBV · Glutamate receptor 2: “Cryo-EM structure of GLUA2 bound to antagonist ZK200775 at 6.8 ångström resolution”. Electron microscopy, 2 ligands (ZK1, NAG), 20 pockets (best druggability 0.84). MolNFT v1 #124324 on GenesisL1: 3D…
- PDB
- 5KBV
- Type
- protein
- Length
- 3,119 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- ZK1, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 782 | 40% helix, 17% strand | P19491 |
| B, C, D | Glutamate receptor 2 | protein | 779 | 40% helix, 17% strand | P19491 |
Ligands and binding sites
- ZK1 · {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.84 | 0.85 | 107 | ZK1 |
| 2 | 953 | 0.84 | 0.85 | 123 | ZK1 |
| 3 | 848 | 0.77 | 0.80 | 102 | empty |
| 4 | 802 | 0.71 | 0.77 | 74 | empty |
| 5 | 503 | 0.71 | 0.80 | 53 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3010 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2974 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2596 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 2547 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 257 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5KBV · Cryo-EM structure of GluA2 bound to antagonist ZK200775 at 6.8 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
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 5KBV · PDBe 5KBV · UniProt P19491
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