Research workbench
Crystal structure of fdts (TM0449) mutant (H53D) with FAD
Analyse Crystal structure of fdts (TM0449) mutant (H53D) with FAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KAR
- Type
- protein
- Length
- 858 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
- FAD
- Pockets
- 4 · 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 (EC 2.1.1.148) | protein | 214 | 50% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase (EC 2.1.1.148) | protein | 212 | 52% helix, 18% strand | Q9WYT0 |
| C | Thymidylate synthase (EC 2.1.1.148) | protein | 218 | 51% helix, 17% strand | Q9WYT0 |
| D | Thymidylate synthase (EC 2.1.1.148) | protein | 214 | 51% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
- 2PE · Nonaethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.86 | 0.88 | 107 | FAD |
| 2 | 316 | 0.77 | 0.88 | 37 | empty |
| 3 | 329 | 0.76 | 0.87 | 43 | FAD |
| 4 | 277 | 0.71 | 0.86 | 41 | FAD |
Interfaces
6 interfaces between chains.
- B–C · 2168 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2151 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1604 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1422 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 252 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4KAR · Crystal structure of FDTS (TM0449) mutant (H53D) with FAD · 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 4KAR · PDBe 4KAR · UniProt Q9WYT0
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