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Crystal structure of the zinc saturated C-terminal half of bovine lactoferrin at 2.0 a resolution reveals two additional zinc binding sites
Analyse Crystal structure of the zinc saturated C-terminal half of bovine lactoferrin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SDX
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin
- UniProt
- P24627
- Ligands
- NAG, MAN, NDG, BMA, ZN, CO3, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin | protein | 335 | 35% helix, 19% strand | P24627 |
| E | Lactotransferrin | protein | 5 | 0% helix, 0% strand | P24627 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- CO3 · Carbonate ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.73 | 0.86 | 41 | empty |
| 2 | 69 | 0.32 | 0.76 | 20 | empty |
| 3 | 56 | 0.29 | 0.75 | 14 | empty |
| 4 | 55 | 0.29 | 0.74 | 21 | NAG |
| 5 | 53 | 0.27 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–E · 206 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1SDX · Crystal structure of the zinc saturated C-terminal half of bovine lactoferrin at 2.0 A… · 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 1SDX · PDBe 1SDX · UniProt P24627
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