Research workbench
Crystal structure of raga-Q66L-GTP/RAGC-S75N-GDP GTPase heterodimer complex
Analyse Crystal structure of raga-Q66L-GTP/RAGC-S75N-GDP GTPase heterodimer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S6D
- Type
- protein
- Length
- 1,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related GTP-binding protein a; RAS-related GTP-binding protein C
- UniProt
- Q7L523, Q9HB90
- Ligands
- GTP, GDP, 9JE, MG
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related GTP-binding protein a | protein | 300 | 42% helix, 26% strand | Q7L523 |
| C | RAS-related GTP-binding protein C | protein | 284 | 43% helix, 21% strand | Q9HB90 |
| D | RAS-related GTP-binding protein C | protein | 272 | 40% helix, 19% strand | Q9HB90 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains C, D
- 9JE · pentane-1,5-diol · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.77 | 0.82 | 45 | empty |
| 2 | 889 | 0.76 | 0.80 | 62 | empty |
| 3 | 321 | 0.75 | 0.87 | 26 | empty |
| 4 | 50 | 0.71 | 0.99 | 16 | 9JE |
| 5 | 501 | 0.64 | 0.76 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1832 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1462 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 1016 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 158 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6S6D · Crystal structure of RagA-Q66L-GTP/RagC-S75N-GDP GTPase heterodimer complex · the same entry in another collection · chain A against A, 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 0.98
- 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 0.95
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 Q7L523
- Every structure of UniProt Q9HB90
- Elsewhere: RCSB PDB 6S6D · PDBe 6S6D · UniProt Q7L523 · UniProt Q9HB90
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