Research workbench
Crystal structure of beta-mannanase from a symbiotic protist of the termite reticulitermes speratus complexed with gluco-manno- oligosaccharide
Analyse Crystal structure of beta-mannanase from a symbiotic protist of the termite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WDR
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannanase
- EC
- 3.2.1.78
- UniProt
- H7CGE2
- Ligands
- BCT, BGC, BMA, MAN, NA, MG
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannanase (EC 3.2.1.78) | protein | 330 | 37% helix, 15% strand | H7CGE2 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.36 | 0.78 | 19 | empty |
| 2 | 80 | 0.32 | 0.73 | 16 | BMA, BCT, MAN |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3WDR · Crystal structure of beta-mannanase from a symbiotic protist of the termite… · 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 H7CGE2
- Elsewhere: RCSB PDB 3WDR · PDBe 3WDR · UniProt H7CGE2
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