MolNFT v1 · #72282 · protein
Crystal structure of thymidylate synthase X (thyx) from helicobacter pylori with FAD and dump at 2.31A resolution
3N3Y · Thymidylate synthase thyx: “Crystal structure of thymidylate synthase X (thyx) from helicobacter pylori with FAD and dump at 2.31A…”. X-ray diffraction, 2 ligands (UMP, FAD), 11 pockets (best druggability 0.83). MolNFT v1 #72282 on…
- PDB
- 3N3Y
- Type
- protein
- Length
- 834 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase thyx
- EC
- 2.1.1.148
- UniProt
- Q5UVJ4
- Ligands
- UMP, FAD
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 209 | 52% helix, 16% strand | Q5UVJ4 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 208 | 55% helix, 16% strand | Q5UVJ4 |
| D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 208 | 56% helix, 16% strand | Q5UVJ4 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 5 copies · chains A, D, B, C
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
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 | 355 | 0.83 | 0.92 | 38 | FAD, UMP |
| 2 | 293 | 0.83 | 0.94 | 37 | FAD, UMP |
| 3 | 288 | 0.82 | 0.93 | 40 | UMP, FAD |
| 4 | 263 | 0.81 | 0.93 | 41 | empty |
| 5 | 222 | 0.79 | 0.93 | 31 | UMP, FAD |
Interfaces
6 interfaces between chains.
- A–B · 1937 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1932 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1321 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1320 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 462 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3N3Y · Crystal structure of Thymidylate Synthase X (ThyX) from Helicobacter pylori with FAD 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 Q5UVJ4
- Elsewhere: RCSB PDB 3N3Y · PDBe 3N3Y · UniProt Q5UVJ4
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