Research workbench
Crystal structure of mtb thya in complex with dump and raltitrexed
Analyse Crystal structure of mtb thya in complex with dump and raltitrexed in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FOX
- Type
- protein
- Length
- 2,086 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P67044
- Ligands
- D16, UMP
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 35% helix, 26% strand | P67044 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 263 | 36% helix, 26% strand | P67044 |
| E, G | Thymidylate synthase (EC 2.1.1.45) | protein | 260 | 37% helix, 26% strand | P67044 |
| H | Thymidylate synthase (EC 2.1.1.45) | protein | 259 | 35% helix, 25% strand | P67044 |
Ligands and binding sites
- D16 · Tomudex · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.77 | 0.86 | 45 | D16, UMP |
| 2 | 136 | 0.73 | 0.93 | 35 | empty |
| 3 | 413 | 0.72 | 0.82 | 44 | UMP, D16 |
| 4 | 490 | 0.71 | 0.81 | 49 | D16, UMP |
| 5 | 474 | 0.71 | 0.81 | 46 | D16, UMP |
Interfaces
9 interfaces between chains.
- A–B · 2193 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2175 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2172 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2098 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 820 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4FOX · Crystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed · the same entry in another collection · chain G against G, 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 4FOX · PDBe 4FOX · UniProt P67044
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