MolNFT v1 · #106615 · protein
Geph E in complex with a GABA receptor ALPHA3 subunit derived peptide in space group P61
4TK2 · Gephyrin: “Geph E in complex with a GABA receptor ALPHA3 subunit derived peptide in space group P61”. X-ray diffraction, 5 pockets (best druggability 0.81). MolNFT v1 #106615 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4TK2
- Type
- protein
- Length
- 839 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gephyrin; Gamma-aminobutyric acid receptor subunit alpha-3
- EC
- 2.7.7.75, 2.10.1.1
- UniProt
- Q03555, P20236
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 411 | 20% helix, 33% strand | Q03555 |
| B | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 411 | 20% helix, 33% strand | Q03555 |
| C | Gamma-aminobutyric acid receptor subunit alpha-3 | protein | 9 | 0% helix, 0% strand | P20236 |
| D | Gamma-aminobutyric acid receptor subunit alpha-3 | protein | 8 | 0% helix, 0% strand | P20236 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.81 | 0.86 | 63 | empty |
| 2 | 973 | 0.80 | 0.81 | 98 | empty |
| 3 | 517 | 0.80 | 0.86 | 68 | empty |
| 4 | 955 | 0.79 | 0.81 | 98 | empty |
| 5 | 50 | 0.38 | 0.81 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3206 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 601 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 579 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 87 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TK2 · Geph E in complex with a GABA receptor alpha3 subunit derived peptide in space group P61 · the same entry in another collection · chain D against D, TM-score 1.00
- Q03555 · AlphaFold monomer V2.0 prediction for gephyrin (Q03555) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P20236 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-3… · a predicted model of the same protein · chain D against A, TM-score 0.50
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 Q03555
- Every structure of UniProt P20236
- Elsewhere: RCSB PDB 4TK2 · PDBe 4TK2 · UniProt Q03555 · UniProt P20236
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