MolNFT v1 · #65414 · protein
Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound to fdump and FAD
3GWC · Thymidylate synthase thyx: “Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound to fdump and FAD”. X-ray diffraction, 2 ligands (FAD, UFP), 20 pockets (best druggability 0.89). MolNFT v1 #65414 on GenesisL1…
- PDB
- 3GWC
- Type
- protein
- Length
- 1,944 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase thyx
- EC
- 2.1.1.148
- UniProt
- P66930
- Ligands
- FAD, UFP
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 246 | 47% helix, 18% strand | P66930 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 239 | 49% helix, 19% strand | P66930 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 243 | 48% helix, 19% strand | P66930 |
| D, F | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 242 | 49% helix, 19% strand | P66930 |
| E | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 244 | 48% helix, 19% strand | P66930 |
| G | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 245 | 47% helix, 18% strand | P66930 |
| H | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 243 | 49% helix, 19% strand | P66930 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, D, C, E, F, H, G
- UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.89 | 0.90 | 114 | FAD, UFP |
| 2 | 564 | 0.85 | 0.91 | 63 | FAD |
| 3 | 1100 | 0.82 | 0.83 | 90 | empty |
| 4 | 294 | 0.79 | 0.91 | 39 | UFP, FAD |
| 5 | 323 | 0.79 | 0.90 | 40 | UFP, FAD |
Interfaces
15 interfaces between chains.
- A–D · 2179 Ų buried · 30 hydrogen bonds · protein-protein
- E–H · 2105 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2085 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 2077 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1707 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3GWC · Crystal structure of Mycobacterium tuberculosis thymidylate synthase X bound to FdUMP and… · 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 P66930
- Elsewhere: RCSB PDB 3GWC · PDBe 3GWC · UniProt P66930
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