MolNFT v1 · #107244 · protein
Crystal structure of pectate lyase PEL3 from pectobacterium carotovorum with two monomers in the A.U
4U49: “Crystal structure of pectate lyase PEL3 from pectobacterium carotovorum with two monomers in the A.U”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.73). MolNFT v1 #107244 on GenesisL1: 3D structure, binding sites…
- 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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