MolNFT v1 · #129733 · protein
Structure of the legionella pneumophila effector ridl (1-866)
5OT4 · Interaptin: “Structure of the legionella pneumophila effector ridl (1-866)”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #129733 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OT4
- Type
- protein
- Length
- 3,311 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interaptin
- UniProt
- G8UZ99
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interaptin | protein | 846 | 65% helix, 0% strand | G8UZ99 |
| B | Interaptin | protein | 842 | 67% helix, 1% strand | G8UZ99 |
| C | Interaptin | protein | 787 | 60% helix, 1% strand | G8UZ99 |
| D | Interaptin | protein | 836 | 64% helix, 1% strand | G8UZ99 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.73 | 0.99 | 15 | empty |
| 2 | 922 | 0.72 | 0.76 | 83 | empty |
| 3 | 609 | 0.69 | 0.78 | 66 | empty |
| 4 | 105 | 0.63 | 0.88 | 27 | empty |
| 5 | 303 | 0.61 | 0.79 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 941 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 145 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5OT4 · Structure of the Legionella pneumophila effector RidL (1-866) · 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 G8UZ99
- Elsewhere: RCSB PDB 5OT4 · PDBe 5OT4 · UniProt G8UZ99
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