Research workbench
Crystal structure of flavine dependant thymidylate synthase S88A mutant from thermotoga maritima at 1.95 ångström resolution
Analyse Crystal structure of flavine dependant thymidylate synthase S88A mutant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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