Research workbench
Structure of yersinia enterocolitica family 28 exopolygalacturonase
Analyse Structure of yersinia enterocolitica family 28 exopolygalacturonase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UVE
- Type
- protein
- Length
- 1,137 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exopolygalacturonase
- Ligands
- NI, SO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exopolygalacturonase | protein | 571 | 10% helix, 46% strand | — |
| B | Exopolygalacturonase | protein | 566 | 11% helix, 45% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 9 copies · chains A, B
- SO4 · Sulfate ion · ion · 19 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.75 | 0.78 | 120 | NI, SO4 |
| 2 | 371 | 0.63 | 0.78 | 37 | SO4 |
| 3 | 427 | 0.62 | 0.77 | 55 | NI, SO4 |
| 4 | 241 | 0.57 | 0.78 | 24 | empty |
| 5 | 100 | 0.44 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 375 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2UVE · Structure of Yersinia enterocolitica Family 28 Exopolygalacturonase · 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 2UVE · PDBe 2UVE
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