Research workbench
Crystal structure of the HK97 bacteriophage small terminase
Analyse Crystal structure of the HK97 bacteriophage small terminase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z6E
- Type
- protein
- Length
- 307 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Enterobacteria phage HK97
- Molecule
- Terminase small subunit
- UniProt
- Q9MBW4
- Ligands
- IOD
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · resolution 1.4 · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terminase small subunit | protein | 104 | 71% helix, 0% strand | Q9MBW4 |
| B | Terminase small subunit | protein | 102 | 73% helix, 0% strand | Q9MBW4 |
| C | Terminase small subunit | protein | 101 | 73% helix, 0% strand | Q9MBW4 |
Ligands and binding sites
- IOD · Iodide ion · ion · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.57 | 0.86 | 22 | IOD |
| 2 | 67 | 0.56 | 0.88 | 20 | IOD |
| 3 | 61 | 0.28 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1310 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1296 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6Z6E · Crystal structure of the HK97 bacteriophage small terminase · 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 Q9MBW4
- Elsewhere: RCSB PDB 6Z6E · PDBe 6Z6E · UniProt Q9MBW4
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