Research workbench
Structure basis of rilp recruitment by RAB7
Analyse Structure basis of rilp recruitment by RAB7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YHN
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-7; Rab interacting lysosomal protein
- UniProt
- P51149, Q96NA2
- Ligands
- GTP, MG
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-7 | protein | 183 | 30% helix, 26% strand | P51149 |
| B | Rab interacting lysosomal protein | protein | 65 | 80% helix, 0% strand | Q96NA2 |
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 | 172 | 0.52 | 0.79 | 35 | GTP |
| 2 | 92 | 0.37 | 0.76 | 15 | empty |
| 3 | 104 | 0.37 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 722 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1YHN · Structure basis of RILP recruitment by Rab7 · the same entry in another collection · chain A against A, TM-score 1.00
- P51149 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P51149) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q96NA2 · AlphaFold monomer V2.0 prediction for rab-interacting lysosomal protein (Q96NA2) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P51149
- Every structure of UniProt Q96NA2
- Elsewhere: RCSB PDB 1YHN · PDBe 1YHN · UniProt P51149 · UniProt Q96NA2
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