MolNFT v1 · #16547 · protein
Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with FAD and PO4 at 2.45 a resolution
1O2B · Thymidylate synthase thyx: “Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with FAD…”. X-ray diffraction, 2 ligands (FAD, PO4), 5 pockets (best druggability 0.85). MolNFT v1 #16547…
- PDB
- 1O2B
- Type
- protein
- Length
- 854 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
- FAD, PO4
- 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 | 213 | 50% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 215 | 52% helix, 18% strand | Q9WYT0 |
| C | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 214 | 52% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 212 | 53% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
- PO4 · Phosphate ion · ion · 3 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 | 585 | 0.85 | 0.91 | 53 | FAD |
| 2 | 338 | 0.81 | 0.91 | 59 | PO4, FAD |
| 3 | 239 | 0.77 | 0.90 | 40 | PO4 |
| 4 | 263 | 0.73 | 0.87 | 30 | PO4 |
| 5 | 173 | 0.67 | 0.87 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2238 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2173 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1414 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1287 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 199 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1O2B · 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 1O2B · PDBe 1O2B · UniProt Q9WYT0
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