Research workbench
Crystal structure of lacto-N-biosidase lnbx from bifidobacterium longum subsp. longum, ligand-free form
Analyse Crystal structure of lacto-N-biosidase lnbx from bifidobacterium longum subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GQC
- Type
- protein
- Length
- 4,661 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lacto-N-biosidase
- EC
- 3.2.1.140
- UniProt
- A0A024QYS6
- Ligands
- CA, NA
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lacto-N-biosidase (EC 3.2.1.140) | protein | 582 | 8% helix, 34% strand | A0A024QYS6 |
| D, E, F, G, H | Lacto-N-biosidase (EC 3.2.1.140) | protein | 583 | 8% helix, 35% strand | A0A024QYS6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.83 | 0.85 | 111 | empty |
| 2 | 1191 | 0.80 | 0.82 | 129 | empty |
| 3 | 800 | 0.76 | 0.80 | 58 | empty |
| 4 | 838 | 0.75 | 0.79 | 111 | empty |
| 5 | 814 | 0.74 | 0.79 | 58 | empty |
Interfaces
11 interfaces between chains.
- B–F · 993 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 977 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 700 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 690 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 684 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5GQC · Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum… · 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 A0A024QYS6
- Elsewhere: RCSB PDB 5GQC · PDBe 5GQC · UniProt A0A024QYS6
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