Research workbench
Open state GLUA2 in complex with stz after micelle signal subtraction
Analyse Open state GLUA2 in complex with stz after micelle signal subtraction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DLZ
- Type
- protein
- Length
- 3,937 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2,VOLTAGE-dependent calcium channel gamma-2 subunit
- UniProt
- P19491, Q9Y698
- Ligands
- GLU, CYZ
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2,VOLTAGE-dependent calcium channel gamma-2 subunit | protein | 983 | 43% helix, 15% strand | P19491, Q9Y698 |
| B, D | Glutamate receptor 2,VOLTAGE-dependent calcium channel gamma-2 subunit | protein | 985 | 41% helix, 15% strand | P19491, Q9Y698 |
| C | Glutamate receptor 2,VOLTAGE-dependent calcium channel gamma-2 subunit | protein | 984 | 43% helix, 15% strand | P19491, Q9Y698 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- CYZ · Cyclothiazide · ligand · 4 copies · chains A, D, B, C
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 | 1104 | 0.82 | 0.84 | 101 | empty |
| 2 | 665 | 0.80 | 0.85 | 79 | CYZ |
| 3 | 805 | 0.78 | 0.82 | 76 | empty |
| 4 | 838 | 0.78 | 0.82 | 84 | empty |
| 5 | 730 | 0.78 | 0.83 | 84 | CYZ |
Interfaces
5 interfaces between chains.
- C–D · 4383 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 4374 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 3210 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 3202 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 395 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6DLZ · Open state GluA2 in complex with STZ after micelle signal subtraction · the same entry in another collection · chain B against B, 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 0.71
- Q9Y698 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-2 subunit… · a predicted model of the same protein · chain C against A, TM-score 0.19
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 Q9Y698
- Elsewhere: RCSB PDB 6DLZ · PDBe 6DLZ · UniProt P19491 · UniProt Q9Y698
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