MolNFT v1 · #120644 · protein
Crystal structure of ADP bound dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7
5H70 · Probable thymidylate kinase: “Crystal structure of ADP bound dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7”. X-ray diffraction, 2 ligands (ADP, MG), 7 pockets (best druggability 0.60). MolNFT v1 #120644 on GenesisL1: 3D…
- PDB
- 5H70
- 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
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Probable thymidylate kinase (EC 2.7.4.9) | protein | 207 | 55% helix, 13% strand | Q970Q8 |
| A | Probable thymidylate kinase (EC 2.7.4.9) | protein | 205 | 55% 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.60 | 0.78 | 32 | empty |
| 2 | 56 | 0.54 | 0.88 | 21 | empty |
| 3 | 221 | 0.53 | 0.77 | 31 | EDO, PGE, MG |
| 4 | 116 | 0.44 | 0.78 | 26 | ADP |
| 5 | 98 | 0.43 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- B–A · 963 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5H70 · Crystal structure of ADP bound dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7 · the same entry in another collection · chain B against B, TM-score 1.00
- 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 5H70 · PDBe 5H70 · UniProt Q970Q8
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