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Crystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using pepsin at 2.6 A resolution
Analyse Crystal structure of C-terminal half of lactoferrin obtained by limited… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EVQ
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Bos taurus
- Molecule
- Lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- BCT, NAG, BMA, FE
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactotransferrin (EC 3.4.21.-) | protein | 348 | 35% helix, 18% strand | P24627 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.69 | 0.82 | 60 | empty |
| 2 | 221 | 0.68 | 0.85 | 41 | empty |
| 3 | 288 | 0.57 | 0.77 | 40 | empty |
| 4 | 146 | 0.47 | 0.77 | 30 | empty |
| 5 | 109 | 0.36 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 546 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7EVQ · Crystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using… · 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 P24627
- Elsewhere: RCSB PDB 7EVQ · PDBe 7EVQ · UniProt P24627
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