Research workbench
GLUA2 in complex with its auxiliary subunit CNIH3 in as MAP II - (lbd- tmd-C3(AS) II)- with antagonist ZK200775, without ntd
Analyse GLUA2 in complex with its auxiliary subunit CNIH3 in as MAP II - (lbd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UD4
- Type
- protein
- Length
- 2,044 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2; Protein cornichon homolog 3
- UniProt
- P19491, Q6ZWS4
- Ligands
- ZK1, CLR
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate receptor 2 | protein | 378 | 49% helix, 12% strand | P19491 |
| E, G | Protein cornichon homolog 3 | protein | 132 | 81% helix, 0% strand | Q6ZWS4 |
| F, H | Protein cornichon homolog 3 | protein | 134 | 84% helix, 0% strand | Q6ZWS4 |
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
- CLR · Cholesterol · ligand · 4 copies · chains A, E, B, F, G, C, H, D
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains A, F, D, B, G, H, C, E
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 | 770 | 0.82 | 0.86 | 86 | empty |
| 2 | 826 | 0.79 | 0.82 | 82 | empty |
| 3 | 624 | 0.73 | 0.80 | 58 | ZK1 |
| 4 | 65 | 0.71 | 0.96 | 13 | empty |
| 5 | 333 | 0.65 | 0.80 | 48 | empty |
Interfaces
13 interfaces between chains.
- B–C · 2916 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 2872 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1775 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1773 Ų buried · 5 hydrogen bonds · protein-protein
- B–G · 688 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6UD4 · GluA2 in complex with its auxiliary subunit CNIH3 in AS map II - (LBD-TMD-C3(AS) II)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q6ZWS4 · AlphaFold monomer V2.0 prediction for protein cornichon homolog 3 (Q6ZWS4) · a predicted model of the same protein · chain F against A, TM-score 0.92
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
- Every structure of UniProt Q6ZWS4
- Elsewhere: RCSB PDB 6UD4 · PDBe 6UD4 · UniProt P19491 · UniProt Q6ZWS4
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