Research workbench
Crystal structure of fdts from T. maritima mutant (R174K) with FAD and dump
Analyse Crystal structure of fdts from T. maritima mutant (R174K) with FAD and dump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KAT
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.148
- UniProt
- Q9WYT0
- Ligands
- DU, FDA
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.148) | protein | 218 | 50% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase (EC 2.1.1.148) | protein | 220 | 51% helix, 17% strand | Q9WYT0 |
| C | Thymidylate synthase (EC 2.1.1.148) | protein | 213 | 50% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase (EC 2.1.1.148) | protein | 209 | 53% helix, 19% strand | Q9WYT0 |
Ligands and binding sites
- DU · 2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, D, B, C
- FDA · Dihydroflavine-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
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.87 | 0.90 | 93 | FDA, DU |
| 2 | 394 | 0.83 | 0.91 | 43 | DU, FDA |
| 3 | 327 | 0.80 | 0.90 | 40 | DU, FDA |
| 4 | 170 | 0.70 | 0.89 | 22 | FDA, DU |
| 5 | 73 | 0.52 | 0.85 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2275 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2268 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1440 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1139 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 262 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4KAT · Crystal structure of FDTS from T. maritima mutant (R174K) with FAD and dUMP · 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 4KAT · PDBe 4KAT · UniProt Q9WYT0
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