MolNFT v1 · #163547 · protein
Crystal structure of raga-Q66L/RAGC-T90N GTPase heterodimer complex
6S6A · RAS-related GTP-binding protein a: “Crystal structure of raga-Q66L/RAGC-T90N GTPase heterodimer complex”. X-ray diffraction, 4 ligands (9JE, GTP, GDP), 20 pockets (best druggability 0.77). MolNFT v1 #163547 on GenesisL1: 3D…
- PDB
- 6S6A
- Type
- protein
- Length
- 1,144 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
- 9JE, GTP, GDP, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related GTP-binding protein a | protein | 298 | 42% helix, 26% strand | Q7L523 |
| B | RAS-related GTP-binding protein a | protein | 298 | 42% helix, 26% strand | Q7L523 |
| C | RAS-related GTP-binding protein C | protein | 273 | 43% helix, 22% strand | Q9HB90 |
| D | RAS-related GTP-binding protein C | protein | 275 | 41% helix, 21% strand | Q9HB90 |
Ligands and binding sites
- 9JE · pentane-1,5-diol · ligand · 3 copies · chains A, B, C
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains C, D
- 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
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.77 | 0.80 | 75 | empty |
| 2 | 60 | 0.73 | 0.99 | 17 | 9JE |
| 3 | 320 | 0.73 | 0.85 | 26 | empty |
| 4 | 623 | 0.69 | 0.77 | 37 | empty |
| 5 | 578 | 0.66 | 0.76 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1590 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1457 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1047 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 146 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6S6A · Crystal structure of RagA-Q66L/RagC-T90N GTPase heterodimer complex · the same entry in another collection · chain D against D, 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 B 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 6S6A · PDBe 6S6A · UniProt Q7L523 · UniProt Q9HB90
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