MolNFT v1 · #30958 · protein
Crystal structure of mycobacterium tuberculosis flavin dependent thymidylate synthase (mtb thyx) in the presence of co-factor FAD and substrate analog 5-bromo-2'-deoxyuridine-5'-monophosphate (brdump)
2AF6 · Thymidylate synthase thyx: “Crystal structure of mycobacterium tuberculosis flavin dependent thymidylate synthase (mtb thyx) in the…”. X-ray diffraction, 3 ligands (FAD, BRU, IOD), 20 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 2AF6
- Type
- protein
- Length
- 1,948 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, BRU, IOD
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 245 | 47% helix, 18% strand | P66930 |
| C, D, F | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 242 | 47% helix, 19% strand | P66930 |
| E, H | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 243 | 46% helix, 19% strand | P66930 |
| G | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 246 | 48% helix, 18% strand | P66930 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, D, C, E, F, H, G
- BRU · 5-bromo-2'-deoxyuridine-5'-monophosphate · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- IOD · Iodide ion · ion · 10 copies · chains A, C, D, E, G, F
- GOL · Glycerol · additive · 14 copies · chains A, B, F, C, D, E, H, G
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 | 828 | 0.88 | 0.91 | 90 | FAD, BRU |
| 2 | 783 | 0.87 | 0.90 | 90 | GOL, FAD, BRU |
| 3 | 1104 | 0.82 | 0.84 | 94 | GOL |
| 4 | 309 | 0.80 | 0.91 | 38 | FAD, BRU |
| 5 | 371 | 0.79 | 0.89 | 40 | FAD, BRU, GOL |
Interfaces
15 interfaces between chains.
- A–D · 2167 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2124 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 2108 Ų buried · 29 hydrogen bonds · protein-protein
- E–H · 2080 Ų buried · 30 hydrogen bonds · protein-protein
- F–H · 1676 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2AF6 · Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase… · 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 2AF6 · PDBe 2AF6 · UniProt P66930
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