MolNFT v1 · #107855 · protein
Crystal structure of native human thymidylate synthase in active form
4UP1: “Crystal structure of native human thymidylate synthase in active form”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.65). MolNFT v1 #107855 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UP1
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Thymidylate synthase (EC 2.1.1.45) | protein | 283 | 34% helix, 24% strand | P04818 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 35% helix, 24% strand | P04818 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.65 | 0.78 | 40 | SO4 |
| 2 | 405 | 0.64 | 0.78 | 40 | SO4 |
| 3 | 375 | 0.62 | 0.77 | 38 | SO4 |
| 4 | 363 | 0.61 | 0.77 | 31 | SO4 |
| 5 | 281 | 0.54 | 0.76 | 31 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 2294 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2291 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 466 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UP1 · Crystal structure of native human Thymidylate synthase in active form · 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 P04818
- Elsewhere: RCSB PDB 4UP1 · PDBe 4UP1 · UniProt P04818
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