MolNFT v1 · #101719 · protein
Crystal structure (type-2) of dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7
4NZY · Probable thymidylate kinase: “Crystal structure (type-2) of dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.66). MolNFT v1 #101719 on GenesisL1: 3D structure…
- PDB
- 4NZY
- Type
- protein
- Length
- 414 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
- PO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable thymidylate kinase (EC 2.7.4.9) | protein | 209 | 54% helix, 12% strand | Q970Q8 |
| B | Probable thymidylate kinase (EC 2.7.4.9) | protein | 205 | 56% helix, 12% strand | Q970Q8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains B
- 1PE · Pentaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.66 | 0.77 | 47 | EDO |
| 2 | 238 | 0.55 | 0.78 | 41 | PO4, PEG, EDO |
Interfaces
1 interface between chains.
- A–B · 1072 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4NZY · Crystal structure (type-2) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7 · the same entry in another collection · chain A against A, 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 0.97
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 4NZY · PDBe 4NZY · UniProt Q970Q8
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