Research workbench
Crystal structure of phosphorylated RAB8A in complex with the rab- binding domain of RILPL2
Analyse Crystal structure of phosphorylated RAB8A in complex with the rab- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RIR
- Type
- protein
- Length
- 412 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-8A; Rilp-like protein 2
- UniProt
- P61006, Q969X0
- Ligands
- GTP, MG
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 173 | 38% helix, 28% strand | P61006 |
| B | RAS-related protein rab-8A | protein | 175 | 38% helix, 28% strand | P61006 |
| D | Rilp-like protein 2 | protein | 32 | 72% helix, 3% strand | Q969X0 |
| C | Rilp-like protein 2 | protein | 32 | 72% helix, 3% strand | Q969X0 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.61 | 0.78 | 46 | GTP, MG |
| 2 | 318 | 0.61 | 0.79 | 42 | GTP, MG |
| 3 | 92 | 0.35 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- D–C · 1053 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 541 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 538 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 264 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6RIR · Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2 · the same entry in another collection · chain C against C, TM-score 1.00
- P61006 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-8A (P61006) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q969X0 · AlphaFold monomer V2.0 prediction for rilp-like protein 2 (Q969X0) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 P61006
- Every structure of UniProt Q969X0
- Elsewhere: RCSB PDB 6RIR · PDBe 6RIR · UniProt P61006 · UniProt Q969X0
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