Research workbench
Crystal structure of human thymidylate kinase with ddtmp and appnhp
Analyse Crystal structure of human thymidylate kinase with ddtmp and appnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NN1
- Type
- protein
- Length
- 209 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to thymidylate kinase (dtmp kinase)
- EC
- 2.7.4.9
- UniProt
- P23919
- Ligands
- 2DT, ANP, MG
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Similar to thymidylate kinase (dtmp kinase) (EC 2.7.4.9) | protein | 209 | 48% 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.63 | 0.82 | 29 | MG, 2DT |
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 1NN1 · PDBe 1NN1 · UniProt P23919
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