MolNFT v1 · #35041 · protein
Structure of the complex of lactoferrin C-lobe with melibiose at 2.0 a resolution
2DYX · Lactotransferrin: “Structure of the complex of lactoferrin C-lobe with melibiose at 2.0 a resolution”. X-ray diffraction, 9 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.74). MolNFT v1 #35041 on GenesisL1: 3D structure…
- PDB
- 2DYX
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin
- UniProt
- P24627
- Ligands
- NAG, BMA, MAN, BGC, GAL, ZN, FE, CO3, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin | protein | 341 | 33% helix, 18% strand | P24627 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- FE · Fe (III) ion · metal · 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 | 274 | 0.74 | 0.87 | 39 | empty |
| 2 | 86 | 0.31 | 0.73 | 28 | NAG |
| 3 | 59 | 0.30 | 0.75 | 12 | empty |
| 4 | 59 | 0.29 | 0.74 | 12 | empty |
| 5 | 63 | 0.28 | 0.73 | 19 | empty |
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2DYX · Structure of the complex of lactoferrin C-lobe with melibiose at 2.0 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 2DYX · PDBe 2DYX · UniProt P24627
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