Research workbench
Structural insights into the loss of catalytic competence in pectate lyase at low pH
Analyse Structural insights into the loss of catalytic competence in pectate lyase at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AMV
- Type
- protein
- Length
- 399 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate lyase
- UniProt
- P39116
- Ligands
- ADA, CA
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate lyase | protein | 399 | 19% helix, 31% strand | P39116 |
Ligands and binding sites
- ADA · alpha-D-galactopyranuronic acid · sugar · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.46 | 0.74 | 27 | empty |
Compared structures
- 5AMV · Structural insights into the loss of catalytic competence in pectate lyase at low pH · the same entry in another collection · chain A against A, TM-score 1.00
- P39116 · AlphaFold monomer V2.0 prediction for pectate lyase (P39116) · a predicted model of the same protein · 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 P39116
- Elsewhere: RCSB PDB 5AMV · PDBe 5AMV · UniProt P39116
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