Research workbench
Crystal structure of ADP bound dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7
Analyse Crystal structure of ADP bound dtmp kinase (ST1543) from sulfolobus tokodaii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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