Research workbench
Crystal structure of thymidylate synthase from burkholderia thailandensis
Analyse Crystal structure of thymidylate synthase from burkholderia thailandensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V8H
- Type
- protein
- Length
- 1,201 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- Q2SXY2
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 312 | 38% helix, 29% strand | Q2SXY2 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 311 | 38% helix, 29% strand | Q2SXY2 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 288 | 35% helix, 31% strand | Q2SXY2 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 290 | 38% helix, 31% strand | Q2SXY2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, B, C
- CIT · Citric acid · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.70 | 0.90 | 33 | empty |
| 2 | 120 | 0.66 | 0.90 | 33 | empty |
| 3 | 349 | 0.64 | 0.79 | 34 | empty |
| 4 | 376 | 0.64 | 0.79 | 36 | EDO |
| 5 | 95 | 0.64 | 0.90 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2898 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2832 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 263 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3V8H · Crystal structure of Thymidylate Synthase from Burkholderia thailandensis · 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 Q2SXY2
- Elsewhere: RCSB PDB 3V8H · PDBe 3V8H · UniProt Q2SXY2
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