MolNFT v1 · #125996 · protein
Structure of human RAB10 in complex with the bmerb domain of mical-1
5LPN · RAS-related protein rab-10: “Structure of human RAB10 in complex with the bmerb domain of mical-1”. X-ray diffraction, 2 ligands (GNP, MG), 6 pockets (best druggability 0.72). MolNFT v1 #125996 on GenesisL1: 3D structure, binding…
- PDB
- 5LPN
- Type
- protein
- Length
- 470 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-10; Protein-methionine sulfoxide oxidase MICAL1
- EC
- 1.14.13.-
- UniProt
- P61026, Q8TDZ2
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-10 | protein | 171 | 36% helix, 29% strand | P61026 |
| B | Protein-methionine sulfoxide oxidase MICAL1 (EC 1.14.13.-) | protein | 132 | 95% helix, 0% strand | Q8TDZ2 |
| C | RAS-related protein rab-10 | protein | 167 | 35% helix, 23% strand | P61026 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.72 | 0.78 | 86 | MG, GNP |
| 2 | 457 | 0.71 | 0.81 | 52 | MG, GNP |
| 3 | 178 | 0.55 | 0.79 | 23 | empty |
| 4 | 74 | 0.52 | 0.85 | 16 | empty |
| 5 | 117 | 0.42 | 0.76 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1288 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 804 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5LPN · Structure of human Rab10 in complex with the bMERB domain of Mical-1 · the same entry in another collection · chain B against B, 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 0.99
- Q8TDZ2 · AlphaFold monomer V2.0 prediction for [F-actin]-monooxygenase MICAL1 (Q8TDZ2) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 Q8TDZ2
- Elsewhere: RCSB PDB 5LPN · PDBe 5LPN · UniProt P61026 · UniProt Q8TDZ2
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