Research workbench
Metal substitution in transferrins: the crystal structure of human copper-lactoferrin at 2.1 ångströms resolution
Analyse Metal substitution in transferrins: the crystal structure of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LFI
- Type
- protein
- Length
- 691 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoferrin
- UniProt
- P02788
- Ligands
- NAG, FUL, FUC, CU, CO3
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoferrin | protein | 691 | 33% helix, 18% strand | P02788 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FUL · beta-L-fucopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- CU · Copper (II) ion · metal · 2 copies · chains A
- CO3 · Carbonate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.78 | 0.90 | 41 | empty |
| 2 | 228 | 0.75 | 0.90 | 37 | empty |
| 3 | 274 | 0.63 | 0.80 | 32 | empty |
| 4 | 302 | 0.58 | 0.77 | 47 | empty |
| 5 | 182 | 0.48 | 0.76 | 28 | empty |
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1LFI · Metal substitution in transferrins: the crystal structure of human copper-lactoferrin at… · the same entry in another collection · chain A against A, TM-score 1.00
- P02788 · AlphaFold monomer V2.0 prediction for lactotransferrin (P02788) · a predicted model of the same protein · 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 P02788
- Elsewhere: RCSB PDB 1LFI · PDBe 1LFI · UniProt P02788
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