Research workbench
Cryo-EM structure of GATOR1
Analyse Cryo-EM structure of GATOR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CET
- Type
- protein
- Length
- 1,741 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gator complex protein NPRL2; Gator complex protein NPRL3; Gator complex protein DEPDC5
- UniProt
- Q8WTW4, Q12980, O75140
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 29% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Gator complex protein NPRL2 | protein | 321 | 35% helix, 18% strand | Q8WTW4 |
| M | Gator complex protein NPRL3 | protein | 519 | 36% helix, 7% strand | Q12980 |
| D | Gator complex protein DEPDC5 | protein | 901 | 23% helix, 23% strand | O75140 |
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 | 1086 | 0.84 | 0.85 | 111 | empty |
| 2 | 838 | 0.83 | 0.85 | 105 | empty |
| 3 | 1107 | 0.83 | 0.83 | 98 | empty |
| 4 | 694 | 0.82 | 0.86 | 77 | empty |
| 5 | 492 | 0.80 | 0.87 | 62 | empty |
Interfaces
3 interfaces between chains.
- N–M · 1853 Ų buried · 19 hydrogen bonds · protein-protein
- N–D · 1663 Ų buried · 4 hydrogen bonds · protein-protein
- M–D · 106 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6CET · Cryo-EM structure of GATOR1 · the same entry in another collection · chain N against N, TM-score 1.00
- O75140 · AlphaFold monomer V2.0 prediction for gator complex protein DEPDC5 (O75140) · a predicted model of the same protein · chain D against A, TM-score 0.81
- Q8WTW4 · AlphaFold monomer V2.0 prediction for gator complex protein NPRL2 (Q8WTW4) · a predicted model of the same protein · chain N against A, TM-score 0.71
- Q12980 · AlphaFold monomer V2.0 prediction for gator complex protein NPRL3 (Q12980) · a predicted model of the same protein · chain M against A, TM-score 0.44
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 Q8WTW4
- Every structure of UniProt Q12980
- Every structure of UniProt O75140
- Elsewhere: RCSB PDB 6CET · PDBe 6CET · UniProt Q8WTW4 · UniProt Q12980 · UniProt O75140
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