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The crystal structure of lactoferrin binding protein B (lbpb) from neisseria meningitidis in complex with human lactoferrin
Analyse The crystal structure of lactoferrin binding protein B (lbpb) from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JRD
- Type
- protein
- Length
- 1,254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoferrin-binding protein B; Lactotransferrin
- UniProt
- Q9JYK4, W8QEY1
- Ligands
- BCT, FE, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoferrin-binding protein B | protein | 566 | 6% helix, 41% strand | Q9JYK4 |
| B | Lactotransferrin | protein | 688 | 35% helix, 18% strand | W8QEY1 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains B
- FE · Fe (III) ion · metal · 2 copies · chains B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.83 | 0.92 | 57 | SO4 |
| 2 | 159 | 0.81 | 0.97 | 26 | empty |
| 3 | 164 | 0.57 | 0.81 | 30 | empty |
| 4 | 251 | 0.56 | 0.77 | 29 | empty |
| 5 | 316 | 0.54 | 0.75 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 1885 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7JRD · The crystal structure of lactoferrin binding protein B (LbpB) from Neisseria meningitidis… · 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 Q9JYK4
- Every structure of UniProt W8QEY1
- Elsewhere: RCSB PDB 7JRD · PDBe 7JRD · UniProt Q9JYK4 · UniProt W8QEY1
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