Research workbench
Crystal structure of the mtb thya in complex with 5-fluoro-dump
Analyse Crystal structure of the mtb thya in complex with 5-fluoro-dump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FOA
- Type
- protein
- Length
- 1,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P67044
- Ligands
- UFP
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 36% helix, 26% strand | P67044 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 258 | 37% helix, 26% strand | P67044 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 260 | 35% helix, 26% strand | P67044 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 36% helix, 26% strand | P67044 |
Ligands and binding sites
- UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.72 | 0.80 | 46 | UFP |
| 2 | 222 | 0.71 | 0.87 | 41 | empty |
| 3 | 445 | 0.68 | 0.80 | 44 | UFP |
| 4 | 484 | 0.66 | 0.78 | 35 | UFP |
| 5 | 426 | 0.65 | 0.78 | 35 | UFP |
Interfaces
3 interfaces between chains.
- C–D · 2248 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2035 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 749 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4FOA · Crystal Structure of the Mtb ThyA in Complex with 5-fluoro-dUMP · the same entry in another collection · chain C against C, 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 P67044
- Elsewhere: RCSB PDB 4FOA · PDBe 4FOA · UniProt P67044
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