Research workbench
Crystal structure analysis of pectate lyase peli from erwinia chrysanthemi
Analyse Crystal structure analysis of pectate lyase peli from erwinia chrysanthemi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B4N
- Type
- protein
- Length
- 628 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
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-pectate lyase (EC 4.2.2.2) | protein | 314 | 3% helix, 52% strand | O50325 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 7 copies · 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 | 1033 | 0.78 | 0.80 | 92 | ZN, SO4 |
| 2 | 51 | 0.33 | 0.77 | 14 | empty |
| 3 | 57 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 824 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3B4N · Crystal Structure Analysis 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 3B4N · PDBe 3B4N · UniProt O50325
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