Research workbench
Structure of DOTL(590-659)-dotn derived from legionella pneumophila
Analyse Structure of DOTL(590-659)-dotn derived from legionella pneumophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X42
- Type
- protein
- Length
- 526 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dotn; Icmo (dotl); Icmj (dotn)
- UniProt
- O54599, Q5ZYC6, Q5ZYB7
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dotn | protein | 195 | 51% helix, 11% strand | O54599 |
| B | Icmo (dotl) | protein | 69 | 64% helix, 0% strand | Q5ZYC6 |
| C | Icmj (dotn) | protein | 195 | 52% helix, 11% strand | Q5ZYB7 |
| D | Icmo (dotl) | protein | 67 | 63% helix, 0% strand | Q5ZYC6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.62 | 0.80 | 41 | empty |
| 2 | 240 | 0.53 | 0.76 | 45 | empty |
| 3 | 125 | 0.42 | 0.75 | 27 | empty |
| 4 | 122 | 0.39 | 0.74 | 23 | empty |
| 5 | 68 | 0.34 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1695 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1659 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 224 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 189 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X42 · Structure of DotL(590-659)-DotN derived from Legionella pneumophila · the same entry in another collection · chain A against A, TM-score 1.00
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 O54599
- Every structure of UniProt Q5ZYC6
- Every structure of UniProt Q5ZYB7
- Elsewhere: RCSB PDB 5X42 · PDBe 5X42 · UniProt O54599 · UniProt Q5ZYC6 · UniProt Q5ZYB7
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