Research workbench
Crystal structure of mouse thymidylate synthase in binary complex with a substrate analogue and strong inhibitor, N(4)-hydroxy-2'- deoxycytidine-5'-monophosphate
Analyse Crystal structure of mouse thymidylate synthase in binary complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EIN
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P07607
- Ligands
- NOH
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 283 | 34% helix, 23% strand | P07607 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 34% helix, 23% strand | P07607 |
Ligands and binding sites
- NOH · 2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.75 | 0.81 | 46 | NOH, GOL |
| 2 | 605 | 0.73 | 0.80 | 52 | NOH |
| 3 | 168 | 0.49 | 0.77 | 19 | empty |
| 4 | 82 | 0.44 | 0.80 | 15 | empty |
| 5 | 64 | 0.40 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2218 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4EIN · Crystal structure of mouse thymidylate synthase in binary complex with a substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- P07607 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P07607) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 4EIN · PDBe 4EIN · UniProt P07607
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