MolNFT v1 · #95627 · protein
Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN43/5
4IVQ: “Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN43/5”. X-ray diffraction, 2 ligands (I43, SO4), 11 pockets (best druggability 0.77). MolNFT v1 #95627 on GenesisL1: 3D structure, binding sites…
- PDB
- 4IVQ
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P03176
- Ligands
- I43, SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 313 | 56% helix, 12% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 309 | 58% helix, 12% strand | P03176 |
Ligands and binding sites
- I43 · 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-4-methoxy-1,5-dimethylpyrimidin-2(1H)-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.77 | 0.97 | 19 | I43 |
| 2 | 196 | 0.72 | 0.89 | 31 | SO4 |
| 3 | 248 | 0.70 | 0.85 | 32 | I43, SO4 |
| 4 | 181 | 0.53 | 0.79 | 31 | empty |
| 5 | 108 | 0.52 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1715 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4IVQ · Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with… · the same entry in another collection · chain B against B, 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 P03176
- Elsewhere: RCSB PDB 4IVQ · PDBe 4IVQ · UniProt P03176
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