MolNFT v1 · #106463 · protein
Crystal structure of ADP bound dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7
4RZU · Probable thymidylate kinase: “Crystal structure of ADP bound dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7”. X-ray diffraction, 2 ligands (ADP, MG), 6 pockets (best druggability 0.63). MolNFT v1 #106463 on GenesisL1: 3D…
- PDB
- 4RZU
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q970Q8
- Ligands
- ADP, MG
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Probable thymidylate kinase (EC 2.7.4.9) | protein | 207 | 57% helix, 13% strand | Q970Q8 |
| A | Probable thymidylate kinase (EC 2.7.4.9) | protein | 205 | 57% helix, 13% strand | Q970Q8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.63 | 0.78 | 51 | EDO, PGE |
| 2 | 307 | 0.60 | 0.78 | 34 | empty |
| 3 | 60 | 0.48 | 0.85 | 20 | empty |
| 4 | 117 | 0.46 | 0.78 | 24 | empty |
| 5 | 72 | 0.37 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 1005 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- Q970Q8 · AlphaFold monomer V2.0 prediction for probable thymidylate kinase (Q970Q8) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q970Q8
- Elsewhere: RCSB PDB 4RZU · PDBe 4RZU · UniProt Q970Q8
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