Research workbench
Crystal structure of phospho-RAB8A with the RH2 domain (117-165) of RILPL2
Analyse Crystal structure of phospho-RAB8A with the RH2 domain (117-165) of RILPL2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LWB
- Type
- protein
- Length
- 219 residues
- Chains
- 2
- 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 0.59
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 182 | 38% helix, 26% strand | P61006 |
| D | Rilp-like protein 2 | protein | 37 | 62% helix, 0% strand | Q969X0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.59 | 0.80 | 36 | GTP, MG |
| 2 | 77 | 0.35 | 0.75 | 16 | empty |
| 3 | 68 | 0.29 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–D · 569 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 7LWB · Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2 · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.97
- Q969X0 · AlphaFold monomer V2.0 prediction for rilp-like protein 2 (Q969X0) · a predicted model of the same protein · chain D against A, TM-score 0.81
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 7LWB · PDBe 7LWB · UniProt P61006 · UniProt Q969X0
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