Research workbench
Crystal structure of a DUF4785 family protein (LPG0956) from legionella pneumophila subsp. pneumophila str. philadelphia 1 at 2.00 a resolution
Analyse Crystal structure of a DUF4785 family protein (LPG0956) from legionella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KH9
- Type
- protein
- Length
- 721 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q5ZWX8
- Ligands
- CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 361 | 7% helix, 52% strand | Q5ZWX8 |
| B | Hypothetical protein | protein | 360 | 6% helix, 54% strand | Q5ZWX8 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.79 | 0.81 | 85 | CA |
| 2 | 139 | 0.50 | 0.79 | 29 | empty |
| 3 | 121 | 0.45 | 0.77 | 25 | empty |
| 4 | 65 | 0.35 | 0.77 | 14 | empty |
| 5 | 67 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1092 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4KH9 · Crystal structure of a DUF4785 family protein (lpg0956) from Legionella pneumophila… · 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 Q5ZWX8
- Elsewhere: RCSB PDB 4KH9 · PDBe 4KH9 · UniProt Q5ZWX8
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