MolNFT v1 · #68594 · protein
Removal of sugars and sugars-like molecules from the solution by C- lobe of lactoferrin: crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D- glucopyranose at 1.9 a resolution
3K0V · Lactotransferrin: “Removal of sugars and sugars-like molecules from the solution by C- lobe of lactoferrin: crystal structure of…”. X-ray diffraction, 9 ligands (NAG, MAN, GLC), 5 pockets (best druggability 0.72). MolNFT v1 #68594…
- PDB
- 3K0V
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- NAG, MAN, GLC, GAL, BGC, ZN, FE, SO4, CO3
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 341 | 30% helix, 18% strand | P24627 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- CO3 · Carbonate 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 | 269 | 0.72 | 0.86 | 41 | empty |
| 2 | 60 | 0.31 | 0.75 | 14 | empty |
| 3 | 71 | 0.30 | 0.74 | 13 | empty |
| 4 | 52 | 0.29 | 0.75 | 12 | empty |
| 5 | 55 | 0.25 | 0.72 | 18 | GAL |
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3K0V · Removal of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin… · 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 3K0V · PDBe 3K0V · UniProt P24627
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