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Structural and biochemical evidence for a boat-like transition state in beta-mannosidases
Analyse Structural and biochemical evidence for a boat-like transition state in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VJX
- Type
- protein
- Length
- 1,675 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- EC
- 3.2.1.25
- UniProt
- Q8AAK6
- Ligands
- IFL, CL, BR
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase (EC 3.2.1.25) | protein | 836 | 24% helix, 36% strand | Q8AAK6 |
| B | Beta-mannosidase (EC 3.2.1.25) | protein | 839 | 23% helix, 36% strand | Q8AAK6 |
Ligands and binding sites
- IFL · (3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)piperidin-2-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B
- BR · Bromide ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.77 | 0.81 | 102 | EDO |
| 2 | 601 | 0.77 | 0.83 | 57 | EDO, CL |
| 3 | 286 | 0.74 | 0.87 | 29 | EDO, BR, CL |
| 4 | 810 | 0.69 | 0.75 | 67 | EDO |
| 5 | 629 | 0.67 | 0.76 | 63 | EDO, BR, CL |
Interfaces
1 interface between chains.
- A–B · 742 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2VJX · Structural and biochemical evidence for a boat-like transition state in beta-mannosidases · 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 Q8AAK6
- Elsewhere: RCSB PDB 2VJX · PDBe 2VJX · UniProt Q8AAK6
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