MolNFT v1 · #113689 · protein
Structural insights into the loss of catalytic competence in pectate lyase at low pH
5AMV: “Structural insights into the loss of catalytic competence in pectate lyase at low pH”. X-ray diffraction, 2 ligands (ADA, CA), 1 pocket (best druggability 0.46). MolNFT v1 #113689 on GenesisL1: 3D structure, binding sites and…
- 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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