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Crystal structure of exo-beta-1,3-galactanase from phanerochaete chrysosporium PC1,3GAL43A apo form
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
- 7BYS
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- 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, BMA, CA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Galactan 1,3-beta-galactosidase (EC 3.2.1.145) | protein | 427 | 5% helix, 52% strand | Q50KB2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.82 | 0.83 | 111 | empty |
| 2 | 242 | 0.58 | 0.79 | 27 | empty |
| 3 | 244 | 0.58 | 0.79 | 30 | empty |
| 4 | 184 | 0.54 | 0.79 | 33 | empty |
| 5 | 115 | 0.51 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 695 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 7BYS · 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 7BYS · PDBe 7BYS · UniProt Q50KB2
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