Research workbench
Substrate distorsion by beta-mannanase from pseudomonas cellulosa
Analyse Substrate distorsion by beta-mannanase from pseudomonas cellulosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GVY
- Type
- protein
- Length
- 376 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan endo-1,4-beta-mannosidase
- EC
- 3.2.1.78
- UniProt
- P49424
- Ligands
- MBF, NIN, BMA, ZN, NA
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannan endo-1,4-beta-mannosidase (EC 3.2.1.78) | protein | 376 | 35% helix, 15% strand | P49424 |
Ligands and binding sites
- MBF · 2-deoxy-2-fluoro-beta-D-mannopyranose · ligand · chains A
- NIN · Dinitrophenylene · ligand · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.69 | 0.94 | 18 | empty |
| 2 | 293 | 0.56 | 0.76 | 38 | MBF, BMA, NIN |
Compared structures
- 1GVY · Substrate distorsion by beta-mannanase from Pseudomonas cellulosa · the same entry in another collection · chain A against A, TM-score 1.00
- P49424 · AlphaFold monomer V2.0 prediction for mannan endo-1,4-beta- mannosidase (P49424) · a predicted model of the same protein · 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 P49424
- Elsewhere: RCSB PDB 1GVY · PDBe 1GVY · UniProt P49424
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