MolNFT v1 · #163025 · protein
Crystal structure of GH125 1,6-alpha-mannosidase from clostridium perfringens in complex with mannoimidazole
6RQK · Alpha-1,6-mannosidase: “Crystal structure of GH125 1,6-alpha-mannosidase from clostridium perfringens in complex with mannoimidazole”. X-ray diffraction, 1 ligand (MVL), 6 pockets (best druggability 0.73). MolNFT v1 #163025 on…
- PDB
- 6RQK
- Type
- protein
- Length
- 849 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannosidase
- UniProt
- Q8XNB2
- Ligands
- MVL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannosidase | protein | 425 | 48% helix, 12% strand | Q8XNB2 |
| B | Alpha-1,6-mannosidase | protein | 424 | 48% helix, 12% strand | Q8XNB2 |
Ligands and binding sites
- MVL · (5R,6R,7S,8R)-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.73 | 0.76 | 79 | empty |
| 2 | 114 | 0.54 | 0.83 | 22 | MVL |
| 3 | 122 | 0.54 | 0.82 | 23 | MVL |
| 4 | 115 | 0.40 | 0.75 | 17 | empty |
| 5 | 123 | 0.38 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 240 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6RQK · Crystal structure of GH125 1,6-alpha-mannosidase from Clostridium perfringens in complex… · 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 Q8XNB2
- Elsewhere: RCSB PDB 6RQK · PDBe 6RQK · UniProt Q8XNB2
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