Research workbench
Structure of Yersinia enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid
Analyse Structure of Yersinia enterocolitica Family 28 Exopolygalacturonase in Complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UVF
- Type
- protein
- Length
- 1,138 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- YERSINIA ENTEROCOLITICA
- Molecule
- Exopolygalacturonase
- Ligands
- ADA, NI, SO4
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exopolygalacturonase | protein | 571 | 12% helix, 44% strand | — |
| B | Exopolygalacturonase | protein | 567 | 11% helix, 45% strand | — |
Ligands and binding sites
- ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A
- NI · Nickel (II) ion · metal · 10 copies · chains A, B
- SO4 · Sulfate ion · ion · 18 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.67 | 0.80 | 60 | SO4, NI |
| 2 | 421 | 0.66 | 0.79 | 52 | SO4, ACT |
| 3 | 365 | 0.58 | 0.76 | 37 | ADA |
| 4 | 193 | 0.58 | 0.81 | 25 | empty |
| 5 | 207 | 0.58 | 0.80 | 30 | NI, ACT |
Interfaces
1 interface between chains.
- A–B · 337 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2UVF · Structure of yersinia enterocolitica family 28 exopolygalacturonase in complex with… · 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
- Elsewhere: RCSB PDB 2UVF · PDBe 2UVF
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