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Crystal structure of beta-mannanase from streptomyces thermolilacinus with mannohexaose
Analyse Crystal structure of beta-mannanase from streptomyces thermolilacinus with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y7E
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase
- EC
- 3.2.1.4
- UniProt
- F5HR99
- Ligands
- BMA, CA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoglucanase (EC 3.2.1.4) | protein | 302 | 36% helix, 19% strand | F5HR99 |
| B | Endoglucanase (EC 3.2.1.4) | protein | 298 | 37% helix, 19% strand | F5HR99 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 17 copies · chains A, B
- CA · Calcium ion · metal · 5 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.58 | 0.85 | 29 | GOL |
| 2 | 309 | 0.56 | 0.76 | 36 | BMA |
| 3 | 280 | 0.53 | 0.75 | 36 | BMA, GOL |
| 4 | 75 | 0.41 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4Y7E · Crystal structure of beta-mannanase from Streptomyces thermolilacinus with mannohexaose · 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 F5HR99
- Elsewhere: RCSB PDB 4Y7E · PDBe 4Y7E · UniProt F5HR99
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