MolNFT v1 · #122424 · protein
Flavin-dependent thymidylate synthase R90A variant in complex with FAD and deoxyuridine monophosphate
5IOS · Thymidylate synthase thyx: “Flavin-dependent thymidylate synthase R90A variant in complex with FAD and deoxyuridine monophosphate”. X-ray diffraction, 2 ligands (FAD, UMP), 4 pockets (best druggability 0.89). MolNFT v1 #122424 on…
- PDB
- 5IOS
- Type
- protein
- Length
- 857 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
- Q9WYT0
- Ligands
- FAD, UMP
- Pockets
- 4 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 214 | 51% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 213 | 52% helix, 18% strand | Q9WYT0 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 213 | 50% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 217 | 53% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.89 | 0.90 | 105 | FAD, UMP |
| 2 | 266 | 0.77 | 0.90 | 42 | UMP, FAD |
| 3 | 240 | 0.77 | 0.90 | 37 | UMP |
| 4 | 196 | 0.73 | 0.89 | 37 | UMP |
Interfaces
6 interfaces between chains.
- C–D · 2173 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2166 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1334 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1283 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5IOS · Flavin-dependent thymidylate synthase R90A variant in complex with FAD and deoxyuridine… · 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 Q9WYT0
- Elsewhere: RCSB PDB 5IOS · PDBe 5IOS · UniProt Q9WYT0
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