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Crystal structure of the catalytic domain of pectate lyase peli from erwinia chrysanthemi
Analyse Crystal structure of the catalytic domain of pectate lyase peli from erwinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B90
- Type
- protein
- Length
- 452 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
- ZN, CA, SO4
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-pectate lyase (EC 4.2.2.2) | protein | 226 | 3% helix, 50% strand | O50325 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.66 | 0.75 | 65 | SO4 |
Interfaces
1 interface between chains.
- A–B · 176 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3B90 · Crystal Structure of the Catalytic Domain of Pectate Lyase PelI from Erwinia chrysanthemi · 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 3B90 · PDBe 3B90 · UniProt O50325
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