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Crystal structure of vaccinia virus thymidylate kinase bound to tdp
Analyse Crystal structure of vaccinia virus thymidylate kinase bound to tdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V54
- Type
- protein
- Length
- 407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P68693
- Ligands
- TYD, POP, MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 49% helix, 13% strand | P68693 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 203 | 48% helix, 13% strand | P68693 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · chains B
- MG · Magnesium ion · metal · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.74 | 0.87 | 55 | MG, POP, TYD |
| 2 | 153 | 0.62 | 0.85 | 28 | TYD |
| 3 | 99 | 0.42 | 0.78 | 21 | empty |
| 4 | 81 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2V54 · Crystal structure of vaccinia virus thymidylate kinase bound to TDP · the same entry in another collection · chain A against A, TM-score 1.00
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 P68693
- Elsewhere: RCSB PDB 2V54 · PDBe 2V54 · UniProt P68693
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