Research workbench
Crystal structure of trichinella spiralis thymidylate synthase complexed with dump
Analyse Crystal structure of trichinella spiralis thymidylate synthase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BY6
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- Q9NDD3
- Ligands
- UMP
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 284 | 37% helix, 24% strand | Q9NDD3 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 288 | 36% helix, 24% strand | Q9NDD3 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 36% helix, 24% strand | Q9NDD3 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 282 | 35% helix, 24% strand | Q9NDD3 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, D, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.77 | 0.80 | 105 | UMP, GOL |
| 2 | 664 | 0.71 | 0.78 | 56 | UMP |
| 3 | 566 | 0.70 | 0.79 | 64 | UMP, DTT |
| 4 | 483 | 0.68 | 0.79 | 44 | UMP |
| 5 | 282 | 0.56 | 0.77 | 45 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 2206 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2190 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 335 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 157 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5BY6 · Crystal structure of Trichinella spiralis thymidylate synthase complexed with dUMP · 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 Q9NDD3
- Elsewhere: RCSB PDB 5BY6 · PDBe 5BY6 · UniProt Q9NDD3
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