Research workbench
Crystal structure of human RAB5A A30P mutant complex with GDP and aluminum fluoride
Analyse Crystal structure of human RAB5A A30P mutant complex with GDP and aluminum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N6K
- Type
- protein
- Length
- 167 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-5A
- UniProt
- P20339
- Ligands
- GDP, AF3, MG
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-5A | protein | 167 | 38% helix, 29% strand | P20339 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- AF3 · Aluminum fluoride · ligand · chains A
- MG · Magnesium ion · metal · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.50 | 0.80 | 27 | MG, GDP, AF3 |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 1N6K · Crystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride · the same entry in another collection · chain A against A, TM-score 1.00
- P20339 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-5A (P20339) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P20339
- Elsewhere: RCSB PDB 1N6K · PDBe 1N6K · UniProt P20339
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