MolNFT v1 · #115566 · protein
Crystal structure of an icml-like type IV secretion system protein (LPG0120) from legionella pneumophila subsp. pneumophila str. philadelphia 1 at 2.65 a resolution
5CNL: “Crystal structure of an icml-like type IV secretion system protein (LPG0120) from legionella pneumophila…”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.53). MolNFT v1 #115566 on GenesisL1: 3D structure, binding…
- PDB
- 5CNL
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Icml-like
- UniProt
- Q5ZZ91
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Icml-like | protein | 139 | 33% helix, 39% strand | Q5ZZ91 |
| B | Icml-like | protein | 139 | 33% helix, 40% strand | Q5ZZ91 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.53 | 0.75 | 40 | empty |
| 2 | 142 | 0.49 | 0.78 | 21 | PGE |
| 3 | 93 | 0.37 | 0.75 | 18 | SO4 |
| 4 | 69 | 0.34 | 0.76 | 13 | PGE |
| 5 | 54 | 0.25 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5CNL · Crystal structure of an IcmL-like type IV secretion system protein (lpg0120) from… · 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 Q5ZZ91
- Elsewhere: RCSB PDB 5CNL · PDBe 5CNL · UniProt Q5ZZ91
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