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Crystal structure of beta-1,3-glucanase from phanerochaete chrysosporium (LAM55A)
Analyse Crystal structure of beta-1,3-glucanase 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
- 3EQN
- Type
- protein
- Length
- 1,504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucan 1,3-beta-glucosidase
- EC
- 3.2.1.58
- UniProt
- Q2Z1W1
- Ligands
- NAG, BMA, ZN, NA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucan 1,3-beta-glucosidase (EC 3.2.1.58) | protein | 752 | 7% helix, 45% strand | Q2Z1W1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.57 | 0.75 | 37 | GOL |
| 2 | 137 | 0.50 | 0.79 | 26 | ZN, GOL |
| 3 | 154 | 0.47 | 0.77 | 25 | ZN, GOL, ACT |
| 4 | 68 | 0.39 | 0.79 | 21 | empty |
| 5 | 54 | 0.33 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 210 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3EQN · Crystal structure of beta-1,3-glucanase from Phanerochaete chrysosporium (Lam55A) · 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 Q2Z1W1
- Elsewhere: RCSB PDB 3EQN · PDBe 3EQN · UniProt Q2Z1W1
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