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The crystal structure of arabidopsis thaliana RAC7-ROP9: the first RAS superfamily GTPase from the plant kingdom
Analyse The crystal structure of arabidopsis thaliana RAC7-ROP9: the first RAS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J0V
- Type
- protein
- Length
- 699 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rac-like GTP-binding protein ARAC7
- UniProt
- O82480
- Ligands
- GDP, MG
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rac-like GTP-binding protein ARAC7 | protein | 178 | 36% helix, 21% strand | O82480 |
| B | Rac-like GTP-binding protein ARAC7 | protein | 184 | 35% helix, 23% strand | O82480 |
| C | Rac-like GTP-binding protein ARAC7 | protein | 159 | 39% helix, 21% strand | O82480 |
| D | Rac-like GTP-binding protein ARAC7 | protein | 178 | 37% helix, 21% strand | O82480 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.73 | 0.76 | 76 | empty |
| 2 | 410 | 0.59 | 0.76 | 53 | empty |
| 3 | 210 | 0.58 | 0.80 | 34 | GDP, MG |
| 4 | 194 | 0.56 | 0.80 | 31 | GDP, MG |
| 5 | 168 | 0.55 | 0.80 | 31 | GDP, MG |
Interfaces
5 interfaces between chains.
- C–D · 616 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 594 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 353 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 186 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 185 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2J0V · The crystal structure of Arabidopsis thaliana RAC7-ROP9: the first RAS superfamily GTPase… · the same entry in another collection · chain D against D, TM-score 1.00
- O82480 · AlphaFold monomer V2.0 prediction for rac-like GTP-binding protein ARAC7 (O82480) · 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 O82480
- Elsewhere: RCSB PDB 2J0V · PDBe 2J0V · UniProt O82480
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