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Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of herpes simplex virus type 1 thymidine kinase interacting with (north)-methanocarba-thymidine
Analyse Kinetics and crystal structure of the wild-type and the engineered Y101F mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E2L
- Type
- protein
- Length
- 614 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
- TMC, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 304 | 58% helix, 13% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 310 | 57% helix, 13% strand | P03176 |
Ligands and binding sites
- TMC · 1-[4-hydroxy-5-(hydroxymethyl)bicyclo[3.1.0]hex-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 125 | 0.80 | 0.97 | 23 | TMC |
| 2 | 239 | 0.60 | 0.80 | 31 | SO4, TMC |
| 3 | 172 | 0.52 | 0.79 | 31 | empty |
| 4 | 95 | 0.43 | 0.79 | 22 | empty |
| 5 | 109 | 0.43 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1728 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1E2L · Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes… · 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 1E2L · PDBe 1E2L · UniProt P03176
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