Research workbench
Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with FAD and dump at 1.6 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
- 1O26
- Type
- protein
- Length
- 876 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, FAD
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 219 | 52% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 221 | 52% helix, 17% strand | Q9WYT0 |
| C, D | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 218 | 53% helix, 17% strand | Q9WYT0 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, D, B, C
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.85 | 0.90 | 70 | PGE, UMP, FAD |
| 2 | 352 | 0.83 | 0.92 | 54 | UMP, FAD, PGE |
| 3 | 170 | 0.76 | 0.92 | 26 | empty |
| 4 | 155 | 0.74 | 0.92 | 23 | empty |
| 5 | 60 | 0.42 | 0.81 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2249 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2245 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1361 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1355 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1O26 · Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga… · 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 Q9WYT0
- Elsewhere: RCSB PDB 1O26 · PDBe 1O26 · UniProt Q9WYT0
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