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Structure of the GH99 endo-alpha-mannanase from bacteroides xylanisolvens in complex with mannose-alpha-1,3-1,2-dideoxymannose
Analyse Structure of the GH99 endo-alpha-mannanase from bacteroides xylanisolvens in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M17
- Type
- protein
- Length
- 349 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 71
- UniProt
- D6D1V7
- Ligands
- 7D1, MAN
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 71 | protein | 349 | 35% helix, 17% strand | D6D1V7 |
Ligands and binding sites
- 7D1 · 1,5-anhydro-2-deoxy-D-arabino-hexitol · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.49 | 0.77 | 33 | 7D1, MAN, EDO |
| 2 | 54 | 0.34 | 0.78 | 16 | empty |
| 3 | 58 | 0.34 | 0.78 | 17 | empty |
Compared structures
- 5M17 · Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with… · 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 D6D1V7
- Elsewhere: RCSB PDB 5M17 · PDBe 5M17 · UniProt D6D1V7
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