Research workbench
Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 1)
Analyse Crystal structure of the small terminase oligomerization core domain from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZQM
- Type
- protein
- Length
- 568 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminase small subunit
- UniProt
- Q1EJR8
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Terminase small subunit | protein | 59 | 42% helix, 29% strand | Q1EJR8 |
| B, C, D, F, J | Terminase small subunit | protein | 56 | 45% helix, 30% strand | Q1EJR8 |
| E | Terminase small subunit | protein | 57 | 44% helix, 30% strand | Q1EJR8 |
| H | Terminase small subunit | protein | 55 | 45% helix, 31% strand | Q1EJR8 |
| I | Terminase small subunit | protein | 58 | 43% helix, 29% strand | Q1EJR8 |
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 | 182 | 0.47 | 0.75 | 34 | empty |
| 2 | 116 | 0.41 | 0.75 | 23 | empty |
| 3 | 70 | 0.33 | 0.75 | 15 | empty |
| 4 | 53 | 0.30 | 0.75 | 12 | empty |
| 5 | 50 | 0.24 | 0.72 | 14 | empty |
Interfaces
10 interfaces between chains.
- A–J · 1232 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 1212 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1163 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1144 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1121 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3ZQM · Crystal structure of the small terminase oligomerization core domain from a SPP1-like… · 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 Q1EJR8
- Elsewhere: RCSB PDB 3ZQM · PDBe 3ZQM · UniProt Q1EJR8
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