Research workbench
Human thymidylate synthase complexed with dump and 3-amino-2-benzoyl- 4-METHYLTHIENO[2,3-B]PYRIDIN-6-ol
Analyse Human thymidylate synthase complexed with dump and 3-amino-2-benzoyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HS3
- Type
- protein
- Length
- 1,704 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, KI3
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 289 | 31% helix, 23% strand | P04818 |
| C, F | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 30% helix, 23% strand | P04818 |
| D, E | Thymidylate synthase (EC 2.1.1.45) | protein | 282 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- KI3 · 3-amino-2-benzoyl-4-methylthieno[2,3-b]pyridin-6-ol · ligand · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.82 | 0.84 | 105 | empty |
| 2 | 535 | 0.79 | 0.85 | 59 | UMP, KI3 |
| 3 | 578 | 0.77 | 0.84 | 65 | empty |
| 4 | 516 | 0.75 | 0.83 | 48 | UMP, KI3 |
| 5 | 462 | 0.74 | 0.83 | 54 | empty |
Interfaces
10 interfaces between chains.
- A–D · 469 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 462 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 384 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 333 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5HS3 · Human thymidylate synthase complexed with dUMP and… · 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 5HS3 · PDBe 5HS3 · UniProt P04818
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