MolNFT v1 · #90163 · protein
Crystal structure of mouse thymidylate synthase in ternary complex with dump and tomudex
4EB4: “Crystal structure of mouse thymidylate synthase in ternary complex with dump and tomudex”. X-ray diffraction, 3 ligands (UMP, D16, SO4), 14 pockets (best druggability 0.81). MolNFT v1 #90163 on GenesisL1: 3D structure, binding sites…
- PDB
- 4EB4
- Type
- protein
- Length
- 1,193 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P07607
- Ligands
- UMP, D16, SO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 300 | 33% helix, 22% strand | P07607 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 301 | 33% helix, 22% strand | P07607 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 295 | 33% helix, 22% strand | P07607 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 297 | 34% helix, 22% strand | P07607 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- D16 · Tomudex · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.81 | 0.82 | 91 | empty |
| 2 | 413 | 0.79 | 0.87 | 47 | UMP, D16 |
| 3 | 449 | 0.78 | 0.86 | 59 | UMP, D16 |
| 4 | 499 | 0.73 | 0.82 | 52 | UMP, D16 |
| 5 | 424 | 0.68 | 0.80 | 41 | UMP, D16 |
Interfaces
4 interfaces between chains.
- C–D · 2337 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2279 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 278 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EB4 · Crystal structure of mouse thymidylate synthase in ternary complex with dUMP and Tomudex · the same entry in another collection · chain C against C, TM-score 1.00
- P07607 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P07607) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P07607
- Elsewhere: RCSB PDB 4EB4 · PDBe 4EB4 · UniProt P07607
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