Research workbench
Architecture of fully occupied GLUA2 AMPA receptor - tarp complex elucidated by single particle cryo-electron microscopy
Analyse Architecture of fully occupied GLUA2 AMPA receptor - tarp complex elucidated by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KK2
- Type
- protein
- Length
- 2,309 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2; Voltage-dependent calcium channel gamma-2 subunit
- UniProt
- P19491, Q71RJ2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 408 | 51% helix, 13% strand | P19491 |
| B, C | Glutamate receptor 2 | protein | 406 | 51% helix, 14% strand | P19491 |
| D | Glutamate receptor 2 | protein | 407 | 50% helix, 14% strand | P19491 |
| E | Voltage-dependent calcium channel gamma-2 subunit | protein | 173 | 68% helix, 6% strand | Q71RJ2 |
| F | Voltage-dependent calcium channel gamma-2 subunit | protein | 167 | 70% helix, 7% strand | Q71RJ2 |
| G | Voltage-dependent calcium channel gamma-2 subunit | protein | 174 | 68% helix, 6% strand | Q71RJ2 |
| H | Voltage-dependent calcium channel gamma-2 subunit | protein | 168 | 70% helix, 7% strand | Q71RJ2 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.85 | 0.90 | 73 | empty |
| 2 | 1139 | 0.82 | 0.83 | 113 | empty |
| 3 | 1188 | 0.81 | 0.82 | 120 | empty |
| 4 | 348 | 0.80 | 0.89 | 64 | empty |
| 5 | 965 | 0.80 | 0.81 | 114 | empty |
Interfaces
13 interfaces between chains.
- A–D · 1961 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1939 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1172 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1139 Ų buried · 4 hydrogen bonds · protein-protein
- C–G · 175 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5KK2 · Architecture of fully occupied GluA2 AMPA receptor - TARP complex elucidated by single… · the same entry in another collection · chain F against F, TM-score 1.00
- Q71RJ2 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-2 subunit… · a predicted model of the same protein · chain H against A, TM-score 0.84
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 Q71RJ2
- Elsewhere: RCSB PDB 5KK2 · PDBe 5KK2 · UniProt P19491 · UniProt Q71RJ2
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