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Structural features of native human thymidine phosphorylase and in complex with 5-iodouracil
Analyse Structural features of native human thymidine phosphorylase and in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WK5
- Type
- protein
- Length
- 1,783 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine phosphorylase
- EC
- 2.4.2.4
- UniProt
- P19971
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine phosphorylase (EC 2.4.2.4) | protein | 448 | 47% helix, 16% strand | P19971 |
| B | Thymidine phosphorylase (EC 2.4.2.4) | protein | 447 | 45% helix, 15% strand | P19971 |
| C | Thymidine phosphorylase (EC 2.4.2.4) | protein | 444 | 47% helix, 13% strand | P19971 |
| D | Thymidine phosphorylase (EC 2.4.2.4) | protein | 444 | 44% helix, 15% strand | P19971 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.77 | 0.98 | 28 | empty |
| 2 | 84 | 0.75 | 0.98 | 27 | empty |
| 3 | 80 | 0.73 | 0.97 | 30 | empty |
| 4 | 69 | 0.73 | 0.98 | 26 | empty |
| 5 | 804 | 0.71 | 0.77 | 80 | empty |
Interfaces
4 interfaces between chains.
- A–C · 304 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 290 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WK5 · Structural features of native human thymidine phosphorylase and in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P19971 · AlphaFold monomer V2.0 prediction for thymidine phosphorylase (P19971) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P19971
- Elsewhere: RCSB PDB 2WK5 · PDBe 2WK5 · UniProt P19971
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