Research workbench
Crystal structure of pectate lyase PEL9A
Analyse Crystal structure of pectate lyase PEL9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RU4
- Type
- protein
- Length
- 400 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate lyase
- EC
- 4.2.2.2
- UniProt
- Q47473
- Ligands
- CA
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate lyase (EC 4.2.2.2) | protein | 400 | 5% helix, 29% strand | Q47473 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.38 | 0.76 | 25 | empty |
| 2 | 54 | 0.27 | 0.74 | 16 | empty |
| 3 | 58 | 0.27 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1RU4 · Crystal structure of pectate lyase Pel9A · 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 Q47473
- Elsewhere: RCSB PDB 1RU4 · PDBe 1RU4 · UniProt Q47473
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