Research workbench
Catalytic function and substrate recognition of the pectate lyase from thermotoga maritima
Analyse Catalytic function and substrate recognition of the pectate lyase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZSC
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate trisaccharide-lyase
- EC
- 4.2.2.22
- UniProt
- Q9WYR4
- Ligands
- AQA, ADA, PO4
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate trisaccharide-lyase (EC 4.2.2.22) | protein | 329 | 12% helix, 40% strand | Q9WYR4 |
Ligands and binding sites
- AQA · 4-deoxy-beta-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · 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 | 92 | 0.34 | 0.74 | 17 | empty |
Compared structures
- 3ZSC · Catalytic function and substrate recognition of the pectate lyase from Thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYR4 · AlphaFold monomer V2.0 prediction for pectate trisaccharide-lyase (Q9WYR4) · 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 Q9WYR4
- Elsewhere: RCSB PDB 3ZSC · PDBe 3ZSC · UniProt Q9WYR4
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