Research workbench
Crystal structure of alpha-1-2-mannosidase from enterococcus faecalis V583
Analyse Crystal structure of alpha-1-2-mannosidase from enterococcus faecalis V583 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DWO
- Type
- protein
- Length
- 2,848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,2-mannosidase
- EC
- 3.2.1.-
- UniProt
- Q832K9
- Ligands
- CA, K, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-1,2-mannosidase (EC 3.2.1.-) | protein | 712 | 31% helix, 25% strand | Q832K9 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.76 | 0.78 | 100 | empty |
| 2 | 72 | 0.73 | 0.97 | 22 | empty |
| 3 | 79 | 0.72 | 0.96 | 21 | empty |
| 4 | 74 | 0.72 | 0.96 | 20 | empty |
| 5 | 73 | 0.69 | 0.95 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 636 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 303 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 107 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 69 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DWO · Crystal structure of alpha-1-2-mannosidase from Enterococcus faecalis V583 · the same entry in another collection · chain D against D, 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 Q832K9
- Elsewhere: RCSB PDB 6DWO · PDBe 6DWO · UniProt Q832K9
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