Research workbench
Crystal structure of PLEKHM1 lir-fused human GABARAP_2-117
Analyse Crystal structure of PLEKHM1 lir-fused human GABARAP_2-117 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DPS
- Type
- protein
- Length
- 365 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid…
- UniProt
- Q9Y4G2, O95166
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein | protein | 122 | 32% helix, 21% strand | Q9Y4G2, O95166 |
| B | Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein | protein | 122 | 31% helix, 23% strand | Q9Y4G2, O95166 |
| C | Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein | protein | 121 | 31% helix, 23% strand | Q9Y4G2, O95166 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.51 | 0.77 | 36 | empty |
| 2 | 118 | 0.43 | 0.77 | 23 | empty |
| 3 | 78 | 0.39 | 0.78 | 24 | empty |
| 4 | 54 | 0.34 | 0.78 | 17 | empty |
| 5 | 60 | 0.29 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 395 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 278 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5DPS · Crystal structure of PLEKHM1 LIR-fused human GABARAP_2-117 · the same entry in another collection · chain A against A, TM-score 1.00
- O95166 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor-associated protein… · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q9Y4G2 · AlphaFold monomer V2.0 prediction for pleckstrin homology domain- containing family M… · a predicted model of the same protein · chain B against A, TM-score 0.33
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 Q9Y4G2
- Every structure of UniProt O95166
- Elsewhere: RCSB PDB 5DPS · PDBe 5DPS · UniProt Q9Y4G2 · UniProt O95166
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