Research workbench
Crystal structure of human thymidylate kinase with D4TMP + appnhp
Analyse Crystal structure of human thymidylate kinase with D4TMP + appnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NN5
- Type
- protein
- Length
- 204 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to deoxythymidylate kinase (thymidylate kinase)
- EC
- 2.7.4.9
- UniProt
- P23919
- Ligands
- 2DT, ANP, MG
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Similar to deoxythymidylate kinase (thymidylate kinase) (EC 2.7.4.9) | protein | 204 | 51% helix, 14% strand | P23919 |
Ligands and binding sites
- 2DT · 3'-deoxythymidine-5'-monophosphate · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.61 | 0.82 | 27 | MG, 2DT |
| 2 | 54 | 0.33 | 0.78 | 15 | empty |
Compared structures
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 P23919
- Elsewhere: RCSB PDB 1NN5 · PDBe 1NN5 · UniProt P23919
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.