Research workbench
Crystal structure of the P1 bacteriophage doc toxin (F68S) in complex with the phd antitoxin (L17M/V39A). northeast structural genomics targets ER385-ER386
Analyse Crystal structure of the P1 bacteriophage doc toxin (F68S) in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KH2
- Type
- protein
- Length
- 782 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death on curing protein; Prevent host death protein
- UniProt
- Q06259, Q06253
- Ligands
- PO4, CL
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Death on curing protein | protein | 124 | 69% helix, 0% strand | Q06259 |
| C, D | Death on curing protein | protein | 123 | 67% helix, 0% strand | Q06259 |
| E, F, G, H | Prevent host death protein | protein | 72 | 64% helix, 17% strand | Q06253 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains E, F, G, H
- CL · Chloride ion · ion · chains A, E
- GOL · Glycerol · additive · 3 copies · chains B, H
- HED · 2-hydroxyethyl disulfide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.41 | 0.76 | 15 | empty |
| 2 | 170 | 0.41 | 0.73 | 27 | PO4 |
| 3 | 54 | 0.33 | 0.78 | 9 | PO4 |
Interfaces
7 interfaces between chains.
- E–F · 1537 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1092 Ų buried · 21 hydrogen bonds · protein-protein
- C–G · 1074 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1073 Ų buried · 18 hydrogen bonds · protein-protein
- D–H · 1064 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3KH2 · Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd… · 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 Q06259
- Every structure of UniProt Q06253
- Elsewhere: RCSB PDB 3KH2 · PDBe 3KH2 · UniProt Q06259 · UniProt Q06253
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