MolNFT v1 · #29169 · protein
Gppnhp-bound RAB21 Q53G mutant GTPase
1Z08 · RAS-related protein rab-21: “Gppnhp-bound RAB21 Q53G mutant GTPase”. X-ray diffraction, 2 ligands (GNP, MG), 4 pockets (best druggability 0.56). MolNFT v1 #29169 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1Z08
- Type
- protein
- Length
- 651 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-21
- UniProt
- Q9UL25
- Ligands
- GNP, MG
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-21 | protein | 160 | 38% helix, 28% strand | Q9UL25 |
| B | RAS-related protein rab-21 | protein | 158 | 37% helix, 30% strand | Q9UL25 |
| C | RAS-related protein rab-21 | protein | 167 | 41% helix, 28% strand | Q9UL25 |
| D | RAS-related protein rab-21 | protein | 166 | 43% helix, 27% strand | Q9UL25 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.56 | 0.80 | 33 | MG, GNP |
| 2 | 165 | 0.55 | 0.81 | 30 | MG, GNP |
| 3 | 168 | 0.55 | 0.80 | 31 | MG, GNP |
| 4 | 159 | 0.54 | 0.80 | 29 | MG, GNP |
Interfaces
1 interface between chains.
- B–D · 519 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 Q9UL25
- Elsewhere: RCSB PDB 1Z08 · PDBe 1Z08 · UniProt Q9UL25
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