Research workbench
Biochemical and structural characterisation of a novel manganese- dependent hydroxynitrile lyase from bacteria
Analyse Biochemical and structural characterisation of a novel manganese- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BIF
- Type
- protein
- Length
- 1,048 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.46
- Source
- GRANULICELLA TUNDRICOLA
- Molecule
- Cupin 2 conserved barrel domain protein
- UniProt
- E8WYN5
- Ligands
- MN
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.46 · 1 distinct chain · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Cupin 2 conserved barrel domain protein | protein | 131 | 0% helix, 49% strand | E8WYN5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.88 | 0.89 | 107 | empty |
| 2 | 1199 | 0.87 | 0.88 | 108 | empty |
| 3 | 850 | 0.71 | 0.76 | 96 | empty |
| 4 | 223 | 0.60 | 0.80 | 28 | empty |
| 5 | 291 | 0.59 | 0.78 | 32 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1580 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1569 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1560 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1518 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 610 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4BIF · Biochemical and structural characterisation of a novel manganese-dependent hydroxynitrile… · 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 E8WYN5
- Elsewhere: RCSB PDB 4BIF · PDBe 4BIF · UniProt E8WYN5
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