Research workbench
Amppcp and tmp bound crystal structure of thymidylate kinase (AQ_969) from aquifex aeolicus VF5
Analyse Amppcp and tmp bound crystal structure of thymidylate kinase (AQ_969) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S35
- Type
- protein
- Length
- 389 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- O67099
- Ligands
- ACP, TMP, MG, CL
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 195 | 56% helix, 13% strand | O67099 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 194 | 57% helix, 13% strand | O67099 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.62 | 0.82 | 28 | ACP, TMP, MG |
| 2 | 203 | 0.62 | 0.82 | 31 | ACP, TMP, MG |
| 3 | 82 | 0.53 | 0.84 | 18 | CL |
| 4 | 98 | 0.49 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4S35 · AMPPCP and TMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex… · the same entry in another collection · chain A against A, TM-score 1.00
- O67099 · AlphaFold monomer V2.0 prediction for thymidylate kinase (O67099) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O67099
- Elsewhere: RCSB PDB 4S35 · PDBe 4S35 · UniProt O67099
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