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Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A resolution
Analyse Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EV0
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Bos taurus
- Molecule
- Lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- NAG, BMA, MAN, FE, CO3
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 33% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, P | Lactotransferrin (EC 3.4.21.-) | protein | 348 | 33% helix, 16% strand | P24627 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, P
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains P, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains P, A
- FE · Fe (III) ion · metal · 2 copies · chains A, P
- CO3 · Carbonate ion · ion · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.73 | 0.85 | 48 | empty |
| 2 | 240 | 0.69 | 0.85 | 44 | empty |
| 3 | 367 | 0.59 | 0.76 | 51 | empty |
| 4 | 148 | 0.46 | 0.77 | 30 | empty |
| 5 | 53 | 0.41 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–P · 528 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7EV0 · Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P24627 · AlphaFold monomer V2.0 prediction for lactotransferrin (P24627) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 7EV0 · PDBe 7EV0 · UniProt P24627
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