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A GH76 family enzyme structure
Analyse A GH76 family enzyme structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M77
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannanase
- UniProt
- Q9Z4P9
- Ligands
- 7K2, 7K3
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannanase | protein | 333 | 62% helix, 8% strand | Q9Z4P9 |
| B | Alpha-1,6-mannanase | protein | 335 | 61% helix, 8% strand | Q9Z4P9 |
Ligands and binding sites
- 7K2 · [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannopyranoside · ligand · 2 copies · chains A, B
- 7K3 · 1-thio-alpha-D-mannopyranose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.60 | 0.76 | 44 | EDO |
| 2 | 319 | 0.58 | 0.77 | 36 | 7K2, 7K3 |
| 3 | 217 | 0.57 | 0.79 | 26 | EDO |
| 4 | 198 | 0.54 | 0.79 | 24 | EDO |
| 5 | 81 | 0.37 | 0.76 | 15 | 7K2 |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5M77 · a GH76 family enzyme structure · 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 Q9Z4P9
- Elsewhere: RCSB PDB 5M77 · PDBe 5M77 · UniProt Q9Z4P9
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