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Crystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 a resolution
Analyse Crystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FDW
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- NAG, BMA, FE, CO3
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactotransferrin (EC 3.4.21.-) | protein | 348 | 33% helix, 17% strand | P24627 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.71 | 0.86 | 42 | empty |
| 2 | 329 | 0.70 | 0.83 | 59 | empty |
| 3 | 386 | 0.60 | 0.76 | 52 | empty |
| 4 | 192 | 0.50 | 0.77 | 35 | empty |
| 5 | 121 | 0.42 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 521 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7FDW · Crystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 A resolution · 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 7FDW · PDBe 7FDW · UniProt P24627
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