Research workbench
Structure of thymidylate synthase thyx complexed to a new inhibitor
Analyse Structure of thymidylate synthase thyx complexed to a new inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FZB
- Type
- protein
- Length
- 3,113 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable thymidylate synthase
- EC
- 2.1.1.148
- UniProt
- O41156
- Ligands
- FAD, 0VJ
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 14 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable thymidylate synthase (EC 2.1.1.148) | protein | 191 | 54% helix, 17% strand | O41156 |
| B, G | Probable thymidylate synthase (EC 2.1.1.148) | protein | 188 | 52% helix, 17% strand | O41156 |
| C | Probable thymidylate synthase (EC 2.1.1.148) | protein | 207 | 52% helix, 16% strand | O41156 |
| D | Probable thymidylate synthase (EC 2.1.1.148) | protein | 203 | 53% helix, 16% strand | O41156 |
| E | Probable thymidylate synthase (EC 2.1.1.148) | protein | 206 | 52% helix, 16% strand | O41156 |
| F | Probable thymidylate synthase (EC 2.1.1.148) | protein | 206 | 50% helix, 17% strand | O41156 |
| H | Probable thymidylate synthase (EC 2.1.1.148) | protein | 179 | 54% helix, 18% strand | O41156 |
| I | Probable thymidylate synthase (EC 2.1.1.148) | protein | 193 | 52% helix, 18% strand | O41156 |
| J | Probable thymidylate synthase (EC 2.1.1.148) | protein | 179 | 55% helix, 18% strand | O41156 |
| K, L | Probable thymidylate synthase (EC 2.1.1.148) | protein | 201 | 53% helix, 16% strand | O41156 |
| M | Probable thymidylate synthase (EC 2.1.1.148) | protein | 197 | 51% helix, 17% strand | O41156 |
| N | Probable thymidylate synthase (EC 2.1.1.148) | protein | 177 | 54% helix, 18% strand | O41156 |
| O | Probable thymidylate synthase (EC 2.1.1.148) | protein | 200 | 51% helix, 16% strand | O41156 |
| P | Probable thymidylate synthase (EC 2.1.1.148) | protein | 197 | 51% helix, 17% strand | O41156 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 16 copies · chains A, C, D, B, E, G, H, F, I, K, L, J, M, O, P, N
- 0VJ · 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione · ligand · 16 copies · chains A, C, B, D, E, G, F, H, I, K, J, L, M, O, N, P
- DMS · Dimethyl sulfoxide · additive · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.88 | 0.90 | 135 | FAD, 0VJ |
| 2 | 930 | 0.88 | 0.90 | 123 | FAD, 0VJ |
| 3 | 895 | 0.87 | 0.89 | 123 | FAD, 0VJ |
| 4 | 427 | 0.82 | 0.90 | 62 | FAD, 0VJ |
| 5 | 393 | 0.82 | 0.91 | 48 | FAD, 0VJ |
Interfaces
33 interfaces between chains.
- M–O · 2291 Ų buried · 39 hydrogen bonds · protein-protein
- I–K · 2170 Ų buried · 33 hydrogen bonds · protein-protein
- F–H · 2159 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2146 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 2145 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4FZB · Structure of thymidylate synthase ThyX complexed to a new inhibitor · 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 O41156
- Elsewhere: RCSB PDB 4FZB · PDBe 4FZB · UniProt O41156
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