Research workbench
Lnbase in complex with lnb-nhacaus
Analyse Lnbase in complex with lnb-nhacaus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BXT
- Type
- protein
- Length
- 1,267 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lacto-N-biosidase
- EC
- 3.2.1.140
- UniProt
- B3TLD6
- Ligands
- 4WS, GAL, SO4
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 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 | 31% helix, 24% strand | B3TLD6 |
| B | Lacto-N-biosidase (EC 3.2.1.140) | protein | 634 | 30% helix, 24% strand | B3TLD6 |
Ligands and binding sites
- 4WS · N-{[(1R,2R,3R,7S,7aR)-1,2,7-trihydroxyhexahydro-1H-pyrrolizin-3-yl]methyl}acetamide · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.66 | 0.84 | 28 | 4WS, GAL |
| 2 | 460 | 0.64 | 0.77 | 41 | empty |
| 3 | 441 | 0.63 | 0.77 | 53 | empty |
| 4 | 195 | 0.63 | 0.83 | 29 | 4WS, GAL |
| 5 | 188 | 0.54 | 0.79 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1930 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5BXT · LNBase in complex with LNB-NHAcAUS · 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 5BXT · PDBe 5BXT · UniProt B3TLD6
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