Research workbench
GDP-bound RAB5C GTPase
Analyse GDP-bound RAB5C GTPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z0D
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-5C
- UniProt
- P35278
- Ligands
- GDP, MG, PO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RAS-related protein rab-5C | protein | 165 | 37% helix, 30% strand | P35278 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.74 | 0.83 | 57 | PO4, MG, GDP |
| 2 | 109 | 0.43 | 0.78 | 24 | MG, GDP |
| 3 | 102 | 0.38 | 0.75 | 20 | empty |
| 4 | 50 | 0.35 | 0.79 | 15 | empty |
| 5 | 59 | 0.33 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 762 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 P35278
- Elsewhere: RCSB PDB 1Z0D · PDBe 1Z0D · UniProt P35278
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