Research workbench
Structural and biochemical characterization of yfce, a phosphoesterase from E. COLI
Analyse Structural and biochemical characterization of yfce, a phosphoesterase from E.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SU1
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yfce
- UniProt
- P67095
- Ligands
- ZN, SO4
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein yfce | protein | 184 | 17% helix, 31% strand | P67095 |
| C, D | Hypothetical protein yfce | protein | 182 | 19% helix, 32% strand | P67095 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.60 | 0.74 | 40 | SO4 |
| 2 | 167 | 0.56 | 0.81 | 21 | empty |
| 3 | 110 | 0.41 | 0.76 | 22 | empty |
| 4 | 63 | 0.41 | 0.80 | 12 | empty |
| 5 | 58 | 0.36 | 0.79 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1110 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1099 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 832 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 830 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1SU1 · Structural and biochemical characterization of Yfce, a phosphoesterase from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- P67095 · AlphaFold monomer V2.0 prediction for phosphodiesterase yfce (P67095) · a predicted model of the same protein · 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 P67095
- Elsewhere: RCSB PDB 1SU1 · PDBe 1SU1 · UniProt P67095
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