MolNFT v1 · #122422 · protein
Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine
5IOQ · Thymidylate synthase thyx: “Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine”. X-ray diffraction, 2 ligands (FAD, DUR), 7 pockets (best druggability 0.86). MolNFT v1 #122422 on GenesisL1: 3D structure…
- PDB
- 5IOQ
- Type
- protein
- Length
- 851 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, DUR
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 210 | 50% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 210 | 50% helix, 18% strand | Q9WYT0 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 218 | 50% helix, 17% strand | Q9WYT0 |
| D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 213 | 52% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- DUR · 2'-deoxyuridine · ligand · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 10 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.86 | 0.91 | 76 | FAD, PGE |
| 2 | 325 | 0.78 | 0.89 | 40 | PGE, FAD, DUR |
| 3 | 244 | 0.78 | 0.91 | 39 | PGE, FAD, DUR |
| 4 | 212 | 0.75 | 0.90 | 40 | PGE, FAD, DUR |
| 5 | 171 | 0.74 | 0.91 | 23 | PGE, DUR |
Interfaces
6 interfaces between chains.
- A–B · 2156 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2102 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1202 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1117 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 242 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5IOQ · Flavin-dependent thymidylate synthase 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 5IOQ · PDBe 5IOQ · UniProt Q9WYT0
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