Research workbench
A legionella pneumophila effector LPG2505
Analyse A legionella pneumophila effector LPG2505 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C0Q
- Type
- protein
- Length
- 1,099 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Effector LPG2505
- UniProt
- Q5ZSL2
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Effector LPG2505 | protein | 279 | 71% helix, 0% strand | Q5ZSL2 |
| B | Effector LPG2505 | protein | 274 | 71% helix, 0% strand | Q5ZSL2 |
| C | Effector LPG2505 | protein | 272 | 69% helix, 1% strand | Q5ZSL2 |
| D | Effector LPG2505 | protein | 274 | 68% helix, 3% strand | Q5ZSL2 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.81 | 105 | empty |
| 2 | 1192 | 0.77 | 0.79 | 108 | empty |
| 3 | 676 | 0.73 | 0.79 | 53 | empty |
| 4 | 156 | 0.66 | 0.86 | 28 | empty |
| 5 | 449 | 0.64 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1841 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1757 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 232 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 210 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7C0Q · a Legionella pneumophila effector Lpg2505 · 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 Q5ZSL2
- Elsewhere: RCSB PDB 7C0Q · PDBe 7C0Q · UniProt Q5ZSL2
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