MolNFT v1 · #16543 · protein
Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with FAD and brdump at 2.3 a resolution
1O27 · Thymidylate synthase thyx: “Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with FAD…”. X-ray diffraction, 2 ligands (BRU, FAD), 5 pockets (best druggability 0.85). MolNFT v1 #16543…
- PDB
- 1O27
- Type
- protein
- Length
- 864 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
- BRU, FAD
- 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 | 216 | 51% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 217 | 52% helix, 18% strand | Q9WYT0 |
| C | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 216 | 51% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 215 | 53% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- BRU · 5-bromo-2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, D, B, C
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
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 | 408 | 0.85 | 0.93 | 66 | BRU, FAD |
| 2 | 303 | 0.81 | 0.92 | 40 | empty |
| 3 | 399 | 0.80 | 0.89 | 41 | BRU, FAD |
| 4 | 153 | 0.75 | 0.92 | 33 | BRU |
| 5 | 55 | 0.51 | 0.87 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2221 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2206 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1291 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1O27 · 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 1O27 · PDBe 1O27 · UniProt Q9WYT0
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