Research workbench
Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with dump at 2.4 a resolution
Analyse Crystal structure of thymidylate synthase complementing protein (TM0449) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O25
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase thyx
- EC
- 2.1.1.-
- UniProt
- Q9WYT0
- Ligands
- UMP
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 214 | 51% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 217 | 51% helix, 18% strand | Q9WYT0 |
| C | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 217 | 52% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 213 | 54% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.85 | 0.90 | 60 | empty |
| 2 | 310 | 0.80 | 0.91 | 47 | UMP |
| 3 | 348 | 0.78 | 0.89 | 34 | UMP |
| 4 | 179 | 0.72 | 0.90 | 31 | UMP |
| 5 | 186 | 0.72 | 0.89 | 28 | UMP |
Interfaces
6 interfaces between chains.
- B–C · 2243 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2221 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1418 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1168 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 224 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1O25 · Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga… · the same entry in another collection · chain D against D, 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 Q9WYT0
- Elsewhere: RCSB PDB 1O25 · PDBe 1O25 · UniProt Q9WYT0
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