MolNFT v1 · #64472 · protein
Crystal structure of flavine dependant thymidylate synthase S88A mutant from thermotoga maritima at 1.95 ångström resolution
3G4A · Thymidylate synthase thyx: “Crystal structure of flavine dependant thymidylate synthase S88A mutant from thermotoga maritima at 1.95…”. X-ray diffraction, 2 ligands (UMP, FAD), 5 pockets (best druggability 0.87). MolNFT v1 #64472 on…
- PDB
- 3G4A
- Type
- protein
- Length
- 864 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
- UMP, FAD
- Pockets
- 5 · best druggability 0.87
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 | 218 | 51% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 220 | 52% helix, 17% strand | Q9WYT0 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 214 | 50% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 212 | 53% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, D, B, C
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.87 | 0.90 | 76 | FAD, UMP |
| 2 | 404 | 0.80 | 0.89 | 48 | UMP, FAD |
| 3 | 321 | 0.80 | 0.91 | 40 | UMP, FAD |
| 4 | 290 | 0.75 | 0.88 | 36 | FAD, UMP |
| 5 | 60 | 0.38 | 0.79 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2237 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 2225 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1413 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1119 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3G4A · Crystal structure of flavine dependant thymidylate synthase S88A mutant from Thermotoga… · 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 3G4A · PDBe 3G4A · UniProt Q9WYT0
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