MolNFT v1 · #53502 · protein
Plasmodium falciparum thymidylate kinase in complex with aztmp and ADP
2WWI · Thymidilate kinase, putative: “Plasmodium falciparum thymidylate kinase in complex with aztmp and ADP”. X-ray diffraction, 2 ligands (ATM, ADP), 6 pockets (best druggability 0.70). MolNFT v1 #53502 on GenesisL1: 3D structure…
- PDB
- 2WWI
- Type
- protein
- Length
- 610 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
- ATM, ADP
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidilate kinase, putative (EC 2.7.4.9) | protein | 208 | 45% helix, 15% strand | Q8I4S1 |
| B | Thymidilate kinase, putative (EC 2.7.4.9) | protein | 197 | 45% helix, 16% strand | Q8I4S1 |
| C | Thymidilate kinase, putative (EC 2.7.4.9) | protein | 205 | 43% helix, 15% strand | Q8I4S1 |
Ligands and binding sites
- ATM · 3'-azido-3'-deoxythymidine-5'-monophosphate · ligand · 3 copies · chains A, B, C
- ADP · Adenosine-5'-diphosphate · ligand · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.70 | 0.81 | 56 | ATM, ADP |
| 2 | 228 | 0.67 | 0.84 | 28 | ATM |
| 3 | 194 | 0.63 | 0.83 | 29 | ATM |
| 4 | 144 | 0.43 | 0.76 | 28 | empty |
| 5 | 69 | 0.34 | 0.76 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 760 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 297 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2WWI · Plasmodium falciparum thymidylate kinase in complex with AZTMP 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 2WWI · PDBe 2WWI · UniProt Q8I4S1
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