Research workbench
Plasmodium falciparum thymidylate kinase in complex with a (THIO)UREA-beta-deoxythymidine inhibitor
Analyse Plasmodium falciparum thymidylate kinase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YOF
- Type
- protein
- Length
- 612 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q8I4S1
- Ligands
- 74W, TAM
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 200 | 47% helix, 16% strand | Q8I4S1 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 46% helix, 15% strand | Q8I4S1 |
| C | Thymidylate kinase (EC 2.7.4.9) | protein | 208 | 43% helix, 15% strand | Q8I4S1 |
Ligands and binding sites
- 74W · 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[[(2R,3S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]thiourea · ligand · 3 copies · chains A, B, C
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.65 | 0.78 | 42 | ACT |
| 2 | 253 | 0.64 | 0.82 | 29 | 74W, ACT |
| 3 | 394 | 0.63 | 0.78 | 35 | empty |
| 4 | 201 | 0.61 | 0.82 | 28 | 74W, TAM |
| 5 | 211 | 0.60 | 0.81 | 36 | 74W, TAM |
Interfaces
2 interfaces between chains.
- B–C · 540 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 331 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2YOF · Plasmodium falciparum thymidylate kinase in complex with a (thio)urea… · 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 Q8I4S1
- Elsewhere: RCSB PDB 2YOF · PDBe 2YOF · UniProt Q8I4S1
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