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Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16- M) in complex with beta-glucan tetrasaccharide
Analyse Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16- M) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U0A
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucanase
- EC
- 3.2.1.73
- UniProt
- P23904
- Ligands
- BGC, CA, ZN
- Pockets
- 9 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-glucanase (EC 3.2.1.73) | protein | 214 | 6% helix, 52% strand | P23904 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.52 | 0.84 | 21 | empty |
| 2 | 187 | 0.52 | 0.78 | 23 | BGC |
| 3 | 170 | 0.51 | 0.78 | 24 | BGC |
| 4 | 183 | 0.50 | 0.77 | 22 | BGC |
| 5 | 158 | 0.49 | 0.77 | 23 | BGC |
Interfaces
4 interfaces between chains.
- B–D · 391 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 384 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 354 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1U0A · Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P23904 · AlphaFold monomer V2.0 prediction for beta-glucanase (P23904) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P23904
- Elsewhere: RCSB PDB 1U0A · PDBe 1U0A · UniProt P23904
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