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Crystal structure of exo-beta-1,3-galactanase from phanerochaete chrysosporium PC1,3GAL43A with galactose
Analyse Crystal structure of exo-beta-1,3-galactanase from phanerochaete chrysosporium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BYT
- Type
- protein
- Length
- 427 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactan 1,3-beta-galactosidase
- EC
- 3.2.1.145
- UniProt
- Q50KB2
- Ligands
- NAG, GLA, GAL, CA
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactan 1,3-beta-galactosidase (EC 3.2.1.145) | protein | 427 | 4% helix, 52% strand | Q50KB2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- ACY · Acetic acid · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.57 | 0.78 | 25 | GOL |
| 2 | 88 | 0.47 | 0.81 | 18 | GOL |
| 3 | 95 | 0.45 | 0.80 | 15 | GLA, GOL |
| 4 | 63 | 0.39 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7BYT · Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium… · 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 Q50KB2
- Elsewhere: RCSB PDB 7BYT · PDBe 7BYT · UniProt Q50KB2
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