MolNFT v1 · #58614 · protein
Crystal structure of pectate lyase peli from erwinia chrysanthemi in complex with tetragalacturonic acid
3B8Y · Endo-pectate lyase: “Crystal structure of pectate lyase peli from erwinia chrysanthemi in complex with tetragalacturonic acid”. X-ray diffraction, 3 ligands (ADA, CA, ZN), 3 pockets (best druggability 0.64). MolNFT v1 #58614 on…
- 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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