Research workbench
Crystal structure of the gef and P4M domain of DRRA/SIDM from legionella pneumophila
Analyse Crystal structure of the gef and P4M domain of DRRA/SIDM from legionella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N6O
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide exchange factor
- UniProt
- Q5ZSQ3
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide exchange factor | protein | 303 | 62% helix, 1% strand | Q5ZSQ3 |
| B | Guanine nucleotide exchange factor | protein | 301 | 64% helix, 1% strand | Q5ZSQ3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.69 | 0.76 | 73 | SO4 |
| 2 | 73 | 0.44 | 0.81 | 16 | empty |
| 3 | 107 | 0.42 | 0.77 | 17 | empty |
| 4 | 79 | 0.36 | 0.77 | 18 | SO4 |
| 5 | 75 | 0.36 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 268 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3N6O · Crystal structure of the GEF and P4M domain of DrrA/SidM from Legionella pneumophila · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZSQ3 · AlphaFold monomer V2.0 prediction for multifunctional virulence effector protein drra… · a predicted model of the same protein · chain B 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 Q5ZSQ3
- Elsewhere: RCSB PDB 3N6O · PDBe 3N6O · UniProt Q5ZSQ3
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