Research workbench
Crystal structure of the legionella pneumophila gap domain of lepb
Analyse Crystal structure of the legionella pneumophila gap domain of lepb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I1M
- Type
- protein
- Length
- 854 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lepb
- UniProt
- Q5ZSM7
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lepb | protein | 285 | 58% helix, 4% strand | Q5ZSM7 |
| B | Lepb | protein | 276 | 59% helix, 4% strand | Q5ZSM7 |
| C | Lepb | protein | 293 | 61% helix, 3% strand | Q5ZSM7 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.69 | 0.95 | 18 | empty |
| 2 | 134 | 0.58 | 0.83 | 23 | empty |
| 3 | 233 | 0.55 | 0.78 | 26 | empty |
| 4 | 107 | 0.53 | 0.82 | 20 | empty |
| 5 | 147 | 0.39 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 845 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 285 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4I1M · Crystal structure of the Legionella pneumophila GAP domain of LepB · 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 Q5ZSM7
- Elsewhere: RCSB PDB 4I1M · PDBe 4I1M · UniProt Q5ZSM7
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