Research workbench
Crystal structure of pectate lyase PEL3 from pectobacterium carotovorum with two monomers in the A.U
Analyse Crystal structure of pectate lyase PEL3 from pectobacterium carotovorum with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U49
- Type
- protein
- Length
- 629 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate lyase
- UniProt
- Q47465
- Ligands
- CA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate lyase | protein | 311 | 2% helix, 49% strand | Q47465 |
| B | Pectate lyase | protein | 318 | 3% helix, 49% strand | Q47465 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.73 | 0.78 | 69 | empty |
| 2 | 118 | 0.39 | 0.76 | 21 | empty |
| 3 | 76 | 0.35 | 0.76 | 20 | empty |
| 4 | 103 | 0.35 | 0.74 | 24 | empty |
| 5 | 84 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 323 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4U49 · Crystal structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with two monomers… · 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 Q47465
- Elsewhere: RCSB PDB 4U49 · PDBe 4U49 · UniProt Q47465
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