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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
- 2VQU
- Type
- protein
- Length
- 1,676 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
- NOY, BR, CL
- 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 | 23% helix, 36% strand | Q8AAK6 |
| B | Beta-mannosidase (EC 3.2.1.25) | protein | 840 | 24% helix, 36% strand | Q8AAK6 |
Ligands and binding sites
- NOY · (2R,3S,4R,5R)-5-(hydroxymethyl)piperidine-2,3,4-triol · ligand · 2 copies · chains A, B
- BR · Bromide ion · ion · 12 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 55 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 | 699 | 0.77 | 0.82 | 61 | EDO, BR, CL |
| 2 | 573 | 0.76 | 0.83 | 56 | EDO, CL, BR |
| 3 | 1129 | 0.73 | 0.76 | 92 | EDO, BR |
| 4 | 638 | 0.67 | 0.76 | 57 | EDO |
| 5 | 542 | 0.65 | 0.77 | 44 | EDO, BR, CL |
Interfaces
1 interface between chains.
- A–B · 721 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2VQU · 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 2VQU · PDBe 2VQU · UniProt Q8AAK6
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