MolNFT v1 · #151460 · protein
Structure of VPS34 lir motif (S249E) bound to gabarap
6HOH · Phosphatidylinositol 3-kinase catalytic subunit type 3…: “Structure of VPS34 lir motif (S249E) bound to gabarap”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #151460 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HOH
- Type
- protein
- Length
- 506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 3-kinase catalytic subunit type 3, gamma-aminobutyric acid…
- EC
- 2.7.1.137
- UniProt
- Q8NEB9, O95166
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 3-kinase catalytic subunit type 3, gamma-aminobutyric acid receptor-associated protein (EC 2.7.1.137) | protein | 126 | 29% helix, 21% strand | Q8NEB9, O95166 |
| B | Phosphatidylinositol 3-kinase catalytic subunit type 3, gamma-aminobutyric acid receptor-associated protein (EC 2.7.1.137) | protein | 129 | 32% helix, 20% strand | Q8NEB9, O95166 |
| C | Phosphatidylinositol 3-kinase catalytic subunit type 3, gamma-aminobutyric acid receptor-associated protein (EC 2.7.1.137) | protein | 127 | 29% helix, 23% strand | Q8NEB9, O95166 |
| D | Phosphatidylinositol 3-kinase catalytic subunit type 3, gamma-aminobutyric acid receptor-associated protein (EC 2.7.1.137) | protein | 124 | 29% helix, 21% strand | Q8NEB9, O95166 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.76 | 0.79 | 102 | empty |
| 2 | 293 | 0.56 | 0.76 | 33 | empty |
| 3 | 188 | 0.53 | 0.78 | 34 | empty |
| 4 | 95 | 0.38 | 0.76 | 22 | empty |
| 5 | 62 | 0.36 | 0.79 | 11 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1100 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 430 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 381 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 303 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6HOH · Structure of VPS34 LIR motif (S249E) bound to GABARAP · 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 D against A, TM-score 0.87
- Q8NEB9 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase catalytic subunit… · a predicted model of the same protein · chain C 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 Q8NEB9
- Every structure of UniProt O95166
- Elsewhere: RCSB PDB 6HOH · PDBe 6HOH · UniProt Q8NEB9 · UniProt O95166
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