Research workbench
Human cytomegalovirus terminase nuclease domain
Analyse Human cytomegalovirus terminase nuclease domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N4P
- Type
- protein
- Length
- 873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminase subunit UL89 protein
- UniProt
- P16732
- Ligands
- MG
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terminase subunit UL89 protein | protein | 216 | 42% helix, 28% strand | P16732 |
| B | Terminase subunit UL89 protein | protein | 227 | 40% helix, 25% strand | P16732 |
| C | Terminase subunit UL89 protein | protein | 218 | 41% helix, 26% strand | P16732 |
| D | Terminase subunit UL89 protein | protein | 212 | 42% helix, 27% strand | P16732 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.57 | 0.79 | 36 | empty |
| 2 | 289 | 0.54 | 0.76 | 38 | empty |
| 3 | 55 | 0.51 | 0.87 | 15 | empty |
| 4 | 199 | 0.50 | 0.76 | 32 | empty |
| 5 | 232 | 0.49 | 0.75 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 927 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 927 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 602 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3N4P · Human cytomegalovirus terminase nuclease domain · 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 P16732
- Elsewhere: RCSB PDB 3N4P · PDBe 3N4P · UniProt P16732
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