Research workbench
Structural genomics, the crystal structure of a protein LPG0085 with unknown function (DUF785) from legionella pneumophila subsp. pneumophila str. philadelphia 1.
Analyse Structural genomics, the crystal structure of a protein LPG0085 with unknown… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PMA
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q5ZZC6
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 129 | 7% helix, 63% strand | Q5ZZC6 |
| B | Uncharacterized protein | protein | 127 | 7% helix, 56% strand | Q5ZZC6 |
Ligands and binding sites
- ACT · Acetate ion · additive · 5 copies · chains A, B
- FMT · Formic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.49 | 0.84 | 14 | empty |
| 2 | 80 | 0.48 | 0.82 | 14 | empty |
| 3 | 83 | 0.47 | 0.81 | 18 | ACT, FMT |
| 4 | 70 | 0.39 | 0.79 | 17 | FMT |
| 5 | 103 | 0.38 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 737 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2PMA · Structural Genomics, the crystal structure of a protein Lpg0085 with unknown function… · 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 Q5ZZC6
- Elsewhere: RCSB PDB 2PMA · PDBe 2PMA · UniProt Q5ZZC6
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