MolNFT v1 · #106614 · protein
Geph E in complex with a GABA receptor ALPHA3 subunit derived peptide in space group P21212
4TK1 · Gephyrin: “Geph E in complex with a GABA receptor ALPHA3 subunit derived peptide in space group P21212”. X-ray diffraction, 5 pockets (best druggability 0.84). MolNFT v1 #106614 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4TK1
- Type
- protein
- Length
- 835 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 0.84
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 414 | 19% helix, 35% strand | Q03555 |
| B | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 401 | 20% helix, 34% strand | Q03555 |
| C | Gamma-aminobutyric acid receptor subunit alpha-3 | protein | 11 | 0% helix, 0% strand | P20236 |
| D | Gamma-aminobutyric acid receptor subunit alpha-3 | protein | 9 | 0% helix, 11% strand | P20236 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1104 | 0.84 | 0.85 | 118 | GOL |
| 2 | 1082 | 0.79 | 0.80 | 95 | empty |
| 3 | 875 | 0.78 | 0.81 | 89 | GOL |
| 4 | 140 | 0.73 | 0.92 | 32 | empty |
| 5 | 69 | 0.30 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3649 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 630 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 595 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 164 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TK1 · Geph E in complex with a GABA receptor alpha3 subunit derived peptide in space group… · 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 B against A, TM-score 0.97
- 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 0.41
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 4TK1 · PDBe 4TK1 · UniProt Q03555 · UniProt P20236
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