Research workbench
LNBase in complex with LNB-NHAcCAS
Analyse LNBase in complex with LNB-NHAcCAS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BXS
- Type
- protein
- Length
- 1,265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Bifidobacterium bifidum JCM 1254
- Molecule
- Lacto-N-biosidase
- EC
- 3.2.1.140
- UniProt
- B3TLD6
- Ligands
- GC2, GAL, SO4
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lacto-N-biosidase (EC 3.2.1.140) | protein | 633 | 30% helix, 24% strand | B3TLD6 |
| B | Lacto-N-biosidase (EC 3.2.1.140) | protein | 632 | 31% helix, 24% strand | B3TLD6 |
Ligands and binding sites
- GC2 · 6-acetamido-6-deoxy-castanospermine · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.68 | 0.77 | 74 | empty |
| 2 | 190 | 0.65 | 0.85 | 29 | GAL, GC2 |
| 3 | 208 | 0.64 | 0.84 | 34 | GAL, GC2 |
| 4 | 473 | 0.64 | 0.77 | 56 | empty |
| 5 | 113 | 0.53 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1808 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5BXS · Lnbase in complex with lnb-nhaccas · 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 B3TLD6
- Elsewhere: RCSB PDB 5BXS · PDBe 5BXS · UniProt B3TLD6
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