Research workbench
Cryo-EM structure of GATOR1-rag
Analyse Cryo-EM structure of GATOR1-rag in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CES
- Type
- protein
- Length
- 2,348 residues
- Chains
- 5
- 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, Q7L523, Q9HB90
- Ligands
- GNP
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Gator complex protein NPRL2 | protein | 321 | 37% helix, 18% strand | Q8WTW4 |
| M | Gator complex protein NPRL3 | protein | 519 | 33% helix, 9% strand | Q12980 |
| D | Gator complex protein DEPDC5 | protein | 901 | 23% helix, 23% strand | O75140 |
| A | RAS-related GTP-binding protein a | protein | 300 | 38% helix, 24% strand | Q7L523 |
| C | RAS-related GTP-binding protein C | protein | 307 | 35% helix, 13% strand | Q9HB90 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1043 | 0.82 | 0.83 | 97 | empty |
| 2 | 576 | 0.81 | 0.87 | 68 | empty |
| 3 | 160 | 0.80 | 0.95 | 40 | empty |
| 4 | 828 | 0.80 | 0.82 | 83 | empty |
| 5 | 425 | 0.79 | 0.88 | 52 | empty |
Interfaces
6 interfaces between chains.
- N–M · 2138 Ų buried · 13 hydrogen bonds · protein-protein
- N–D · 1888 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1512 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 954 Ų buried · 12 hydrogen bonds · protein-protein
- M–D · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CES · Cryo-EM structure of GATOR1-RAG · the same entry in another collection · chain C against C, TM-score 1.00
- Q7L523 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein a (Q7L523) · a predicted model of the same protein · chain A against A, TM-score 0.95
- 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 0.82
- Q9HB90 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein C (Q9HB90) · a predicted model of the same protein · chain C against A, TM-score 0.79
- 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 0.72
- 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 0.45
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
- Every structure of UniProt Q7L523
- Every structure of UniProt Q9HB90
- Elsewhere: RCSB PDB 6CES · PDBe 6CES · UniProt Q8WTW4 · UniProt Q12980 · UniProt O75140 · UniProt Q7L523 · UniProt Q9HB90
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