Research workbench
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
- 2VMF
- 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
- MVL, BR, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase (EC 3.2.1.25) | protein | 835 | 23% helix, 37% strand | Q8AAK6 |
| B | Beta-mannosidase (EC 3.2.1.25) | protein | 840 | 24% helix, 36% strand | Q8AAK6 |
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 · 2 copies · chains A, B
- BR · Bromide ion · ion · 16 copies · chains A, B
- CL · Chloride ion · ion · 11 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 40 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.78 | 0.82 | 56 | EDO, CL, BR |
| 2 | 568 | 0.76 | 0.83 | 57 | EDO, BR, CL |
| 3 | 547 | 0.73 | 0.81 | 73 | EDO |
| 4 | 821 | 0.69 | 0.75 | 68 | EDO |
| 5 | 652 | 0.67 | 0.76 | 66 | BR, CL, EDO |
Interfaces
1 interface between chains.
- A–B · 764 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2VMF · 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 2VMF · PDBe 2VMF · UniProt Q8AAK6
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