MolNFT v1 · #97339 · protein
Crystal structure of fdts from T. maritima mutant (H53D) with FAD and dump
4KAS · Thymidylate synthase thyx: “Crystal structure of fdts from T. maritima mutant (H53D) with FAD and dump”. X-ray diffraction, 5 ligands (DU, FAD, SO4), 5 pockets (best druggability 0.85). MolNFT v1 #97339 on GenesisL1: 3D structure…
- PDB
- 4KAS
- Type
- protein
- Length
- 862 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
- DU, FAD, SO4, CL, PO4
- Pockets
- 5 · best druggability 0.85
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 | 213 | 53% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 217 | 52% 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 | 214 | 52% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- DU · 2'-deoxyuridine-5'-monophosphate · ligand · 3 copies · chains A, D, B, C
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains C
- PO4 · Phosphate ion · ion · chains A, D
- 2PE · Nonaethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.85 | 0.91 | 51 | SO4, FAD |
| 2 | 398 | 0.80 | 0.89 | 55 | SO4, PO4 |
| 3 | 397 | 0.80 | 0.89 | 42 | DU, FAD |
| 4 | 297 | 0.79 | 0.90 | 47 | DU, FAD |
| 5 | 334 | 0.75 | 0.87 | 41 | DU |
Interfaces
6 interfaces between chains.
- A–D · 2228 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2205 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1604 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1395 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 239 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4KAS · Crystal structure of FDTS from T. maritima mutant (H53D) 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 4KAS · PDBe 4KAS · UniProt Q9WYT0
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