Research workbench
Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5
Analyse Structure of human diferric lactoferrin at 2.5A resolution using crystals grown… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SQY
- 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, FE, CO3
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoferrin | protein | 691 | 35% helix, 19% strand | P02788 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FE · Fe (III) 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.77 | 0.89 | 37 | empty |
| 2 | 283 | 0.76 | 0.89 | 40 | empty |
| 3 | 374 | 0.62 | 0.78 | 44 | empty |
| 4 | 250 | 0.58 | 0.79 | 41 | empty |
| 5 | 135 | 0.51 | 0.80 | 22 | empty |
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1SQY · Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5 · 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 1SQY · PDBe 1SQY · UniProt P02788
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