MolNFT v1 · #134286 · protein
Structure of human RAB10 in complex with the bmerb domain of mical-cl
5SZJ · RAS-related protein rab-10: “Structure of human RAB10 in complex with the bmerb domain of mical-cl”. X-ray diffraction, 2 ligands (GNP, MG), 2 pockets (best druggability 0.76). MolNFT v1 #134286 on GenesisL1: 3D structure, binding…
- PDB
- 5SZJ
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-10; Mical C-terminal-like protein
- UniProt
- P61026, Q6ZW33
- Ligands
- GNP, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-10 | protein | 175 | 34% helix, 27% strand | P61026 |
| B | Mical C-terminal-like protein | protein | 145 | 92% helix, 0% strand | Q6ZW33 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.76 | 0.79 | 72 | GNP, MG, PEG |
| 2 | 141 | 0.50 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1070 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5SZJ · Structure of human Rab10 in complex with the bMERB domain of Mical-cL · the same entry in another collection · chain A against A, TM-score 1.00
- P61026 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-10 (P61026) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P61026
- Every structure of UniProt Q6ZW33
- Elsewhere: RCSB PDB 5SZJ · PDBe 5SZJ · UniProt P61026 · UniProt Q6ZW33
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