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Crystal structure of pectate lyase peli from erwinia chrysanthemi in complex with tetragalacturonic acid
Analyse Crystal structure of pectate lyase peli from erwinia chrysanthemi in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B8Y
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-pectate lyase
- EC
- 4.2.2.2
- UniProt
- O50325
- Ligands
- ADA, CA, ZN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-pectate lyase (EC 4.2.2.2) | protein | 304 | 2% helix, 54% strand | O50325 |
| B | Endo-pectate lyase (EC 4.2.2.2) | protein | 294 | 2% helix, 57% strand | O50325 |
Ligands and binding sites
- ADA · alpha-D-galactopyranuronic acid · sugar · 8 copies · chains A, B
- CA · Calcium ion · metal · chains B
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.64 | 0.74 | 77 | ADA |
| 2 | 84 | 0.38 | 0.77 | 18 | empty |
| 3 | 74 | 0.38 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 446 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3B8Y · Crystal Structure of Pectate Lyase PelI from Erwinia chrysanthemi 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
- Every structure of UniProt O50325
- Elsewhere: RCSB PDB 3B8Y · PDBe 3B8Y · UniProt O50325
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