MolNFT v1 · #66740 · protein
Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound with FAD
3HZG · Thymidylate synthase thyx: “Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound with FAD”. X-ray diffraction, 2 ligands (FAD, PO4), 13 pockets (best druggability 0.88). MolNFT v1 #66740 on GenesisL1: 3D…
- PDB
- 3HZG
- Type
- protein
- Length
- 978 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
- P66930
- Ligands
- FAD, PO4
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 245 | 46% helix, 18% strand | P66930 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 243 | 48% helix, 19% strand | P66930 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 9 copies · chains A, D, B, C
- GOL · Glycerol · additive · 3 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.88 | 0.91 | 88 | PO4, FAD, GOL |
| 2 | 234 | 0.77 | 0.91 | 28 | PO4, FAD |
| 3 | 243 | 0.77 | 0.91 | 33 | PO4, FAD |
| 4 | 223 | 0.75 | 0.90 | 35 | FAD, PO4 |
| 5 | 152 | 0.60 | 0.84 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2111 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2089 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1703 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1673 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 294 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3HZG · Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound 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 P66930
- Elsewhere: RCSB PDB 3HZG · PDBe 3HZG · UniProt P66930
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