Research workbench
Crystal structure of herpes simplex UL42 bound to the C-terminus of HSV pol
Analyse Crystal structure of herpes simplex UL42 bound to the C-terminus of HSV pol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DML
- Type
- protein
- Length
- 1,233 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase processivity factor; DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P10226, P07917
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase processivity factor | protein | 267 | 13% helix, 42% strand | P10226 |
| B, D, F, H | DNA polymerase (EC 2.7.7.7) | protein | 36 | 64% helix, 11% strand | P07917 |
| C | DNA polymerase processivity factor | protein | 272 | 15% helix, 42% strand | P10226 |
| E, G | DNA polymerase processivity factor | protein | 275 | 16% helix, 42% strand | P10226 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.85 | 0.88 | 106 | empty |
| 2 | 194 | 0.66 | 0.85 | 25 | empty |
| 3 | 186 | 0.66 | 0.86 | 27 | empty |
| 4 | 274 | 0.62 | 0.80 | 32 | empty |
| 5 | 218 | 0.53 | 0.77 | 26 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1413 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1409 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1405 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1401 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 928 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1DML · Crystal structure of herpes simplex UL42 bound to the C-terminus of HSV pol · 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 P10226
- Every structure of UniProt P07917
- Elsewhere: RCSB PDB 1DML · PDBe 1DML · UniProt P10226 · UniProt P07917
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