Research workbench
Structure of legionella pneumophila dotn
Analyse Structure of legionella pneumophila dotn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X1H
- Type
- protein
- Length
- 2,351 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Icmj (dotn)
- UniProt
- Q5ZYB7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Icmj (dotn) | protein | 199 | 46% helix, 10% strand | Q5ZYB7 |
| C, W | Icmj (dotn) | protein | 196 | 48% helix, 12% strand | Q5ZYB7 |
| E, G, I | Icmj (dotn) | protein | 197 | 47% helix, 11% strand | Q5ZYB7 |
| K | Icmj (dotn) | protein | 194 | 48% helix, 11% strand | Q5ZYB7 |
| M, O, Q, S, U | Icmj (dotn) | protein | 195 | 52% helix, 11% strand | Q5ZYB7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, C, E, G, I, K, M, O, Q, S, U, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.74 | 0.80 | 71 | empty |
| 2 | 626 | 0.72 | 0.79 | 56 | empty |
| 3 | 643 | 0.70 | 0.78 | 78 | empty |
| 4 | 589 | 0.67 | 0.77 | 49 | empty |
| 5 | 284 | 0.63 | 0.80 | 40 | empty |
Interfaces
16 interfaces between chains.
- A–C · 1269 Ų buried · 9 hydrogen bonds · protein-protein
- E–W · 1060 Ų buried · 3 hydrogen bonds · protein-protein
- K–M · 1058 Ų buried · 9 hydrogen bonds · protein-protein
- G–Q · 1054 Ų buried · 5 hydrogen bonds · protein-protein
- I–U · 1039 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5X1H · Structure of Legionella pneumophila DotN · 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 Q5ZYB7
- Elsewhere: RCSB PDB 5X1H · PDBe 5X1H · UniProt Q5ZYB7
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