Research workbench
Crystal structure of human thymidylate synthase bound to a peptide inhibitor
Analyse Crystal structure of human thymidylate synthase bound to a peptide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N5E
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase; Synthetic peptide lr
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 263 | 33% helix, 25% strand | P04818 |
| D | Synthetic peptide lr | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.63 | 0.76 | 54 | SO4 |
| 2 | 322 | 0.59 | 0.77 | 39 | SO4 |
| 3 | 97 | 0.43 | 0.78 | 21 | empty |
| 4 | 100 | 0.43 | 0.78 | 15 | empty |
| 5 | 93 | 0.41 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2194 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 496 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 496 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 1 disulfide (methylation, disulfide).
Compared structures
- 3N5E · Crystal Structure of human thymidylate synthase bound to a peptide inhibitor · 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 3N5E · PDBe 3N5E · UniProt P04818
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