MolNFT v1 · #114702 · protein
Lnbase in complex with lnb-nhacdnj
5BXR · Lacto-N-biosidase: “Lnbase in complex with lnb-nhacdnj”. X-ray diffraction, 3 ligands (NOK, GAL, SO4), 15 pockets (best druggability 0.66). MolNFT v1 #114702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BXR
- Type
- protein
- Length
- 1,270 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
- NOK, GAL, SO4
- Pockets
- 15 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lacto-N-biosidase (EC 3.2.1.140) | protein | 634 | 30% helix, 24% strand | B3TLD6 |
| B | Lacto-N-biosidase (EC 3.2.1.140) | protein | 636 | 31% helix, 24% strand | B3TLD6 |
Ligands and binding sites
- NOK · 2-acetamido-1,2-dideoxynojirmycin · 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
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.66 | 0.85 | 28 | GAL, NOK |
| 2 | 466 | 0.63 | 0.77 | 53 | empty |
| 3 | 182 | 0.63 | 0.84 | 32 | GAL, NOK, SO4 |
| 4 | 396 | 0.62 | 0.77 | 41 | empty |
| 5 | 265 | 0.58 | 0.79 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 2001 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5BXR · LNBase in complex with LNB-NHAcDNJ · 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 5BXR · PDBe 5BXR · UniProt B3TLD6
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