Research workbench
Crystal structure of exo-beta-1,3-galactanase from phanerochaete chrysosporium PC1,3GAL43A E208A with beta-1,3-galactotriose
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
- 7BYX
- Type
- protein
- Length
- 1,708 residues
- Chains
- 4
- 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, GAL, MAN, NDG, BMA, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galactan 1,3-beta-galactosidase (EC 3.2.1.145) | protein | 427 | 4% helix, 51% strand | Q50KB2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, C, B, D
- GAL · beta-D-galactopyranose · sugar · 12 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains B, C
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 19 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.88 | 0.90 | 81 | ACT |
| 2 | 1136 | 0.84 | 0.85 | 114 | GOL |
| 3 | 1133 | 0.83 | 0.84 | 104 | ACT, GOL |
| 4 | 1116 | 0.83 | 0.84 | 104 | GOL |
| 5 | 131 | 0.56 | 0.82 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1352 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1274 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 747 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 711 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 4 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7BYX · 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 7BYX · PDBe 7BYX · UniProt Q50KB2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.