MolNFT v1 · #69777 · protein
Crystal structure of RAB1-activation domain and P4M domain of SIDM/DRRA from legionella
3L0M: “Crystal structure of RAB1-activation domain and P4M domain of SIDM/DRRA from legionella”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.71). MolNFT v1 #69777 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3L0M
- Type
- protein
- Length
- 651 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Drra
- UniProt
- Q29ST3
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Drra | protein | 328 | 63% helix, 1% strand | Q29ST3 |
| B | Drra | protein | 323 | 61% helix, 1% strand | Q29ST3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.71 | 0.81 | 50 | SO4 |
| 2 | 590 | 0.67 | 0.77 | 61 | empty |
| 3 | 129 | 0.43 | 0.76 | 26 | empty |
| 4 | 101 | 0.41 | 0.77 | 18 | empty |
| 5 | 85 | 0.41 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3L0M · Crystal structure of Rab1-activation domain and P4M domain of SidM/DrrA from legionella · the same entry in another collection · chain A against A, TM-score 1.00
- Q29ST3 · AlphaFold monomer V2.0 prediction for multifunctional virulence effector protein drra… · 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 Q29ST3
- Elsewhere: RCSB PDB 3L0M · PDBe 3L0M · UniProt Q29ST3
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