Research workbench
Plasmodium falciparum thymidylate kinase in complex with tmp and ADP
Analyse Plasmodium falciparum thymidylate kinase in complex with tmp and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WWF
- Type
- protein
- Length
- 631 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidilate kinase, putative
- EC
- 2.7.4.9
- UniProt
- Q8I4S1
- Ligands
- TMP, ADP, NA
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidilate kinase, putative (EC 2.7.4.9) | protein | 211 | 45% helix, 15% strand | Q8I4S1 |
| B | Thymidilate kinase, putative (EC 2.7.4.9) | protein | 208 | 46% helix, 15% strand | Q8I4S1 |
| C | Thymidilate kinase, putative (EC 2.7.4.9) | protein | 212 | 44% helix, 15% strand | Q8I4S1 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 3 copies · chains A, B, C
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.69 | 0.80 | 56 | TMP, ADP, NA |
| 2 | 208 | 0.63 | 0.83 | 26 | TMP, NA |
| 3 | 238 | 0.63 | 0.82 | 31 | TMP, ADP, NA |
| 4 | 338 | 0.57 | 0.76 | 36 | empty |
| 5 | 62 | 0.30 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 778 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 305 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2WWF · Plasmodium falciparum thymidylate kinase in complex with TMP and ADP · 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 2WWF · PDBe 2WWF · UniProt Q8I4S1
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