Research workbench
Escherichia COLI Y209W apoprotein
Analyse Escherichia COLI Y209W apoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G8X
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P0A884
- Ligands
- CO3, PO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 262 | 33% helix, 26% strand | P0A884 |
Ligands and binding sites
- CO3 · Carbonate ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.71 | 0.78 | 50 | CO3, PO4, DTT |
| 2 | 592 | 0.69 | 0.78 | 46 | CO3, PO4, DTT |
| 3 | 86 | 0.41 | 0.79 | 18 | empty |
| 4 | 112 | 0.41 | 0.76 | 19 | empty |
| 5 | 78 | 0.31 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2338 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 2G8X · Escherichia coli Y209W apoprotein · 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 P0A884
- Elsewhere: RCSB PDB 2G8X · PDBe 2G8X · UniProt P0A884
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