Research workbench
The coordinates of the apo hexameric terminase complex
Analyse The coordinates of the apo hexameric terminase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M5S
- Type
- protein
- Length
- 1,440 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.9
- Source
- Human alphaherpesvirus 1 strain 17
- Molecule
- Tripartite terminase subunit 3; Tripartite terminase subunit 1; Tripartite terminase…
- EC
- 3.1.-.-
- UniProt
- P04295, P10212, B9VQG1
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.84
Structure
electron microscopy · resolution 3.9 · 3 distinct chains · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tripartite terminase subunit 3 (EC 3.1.-.-) | protein | 646 | 38% helix, 12% strand | P04295 |
| B | Tripartite terminase subunit 1 | protein | 689 | 52% helix, 3% strand | P10212 |
| C | Tripartite terminase subunit 2 | protein | 105 | 59% helix, 0% strand | B9VQG1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.84 | 0.88 | 87 | empty |
| 2 | 743 | 0.84 | 0.88 | 89 | empty |
| 3 | 660 | 0.82 | 0.86 | 67 | empty |
| 4 | 287 | 0.79 | 0.91 | 50 | empty |
| 5 | 163 | 0.63 | 0.85 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6553 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 4687 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 850 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6M5S · The coordinates of the apo hexameric terminase complex · 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 P04295
- Every structure of UniProt P10212
- Every structure of UniProt B9VQG1
- Elsewhere: RCSB PDB 6M5S · PDBe 6M5S · UniProt P04295 · UniProt P10212 · UniProt B9VQG1
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