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Crystal structure of C-lobe of bovine lactoferrin complexed with 1,2, 5-pentanetriol at 1.98 a resolution
Analyse Crystal structure of C-lobe of bovine lactoferrin complexed with 1,2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UK4
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin; C-terminal peptide from lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- XXD, NAG, ZN, FE, CO3, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 335 | 34% helix, 18% strand | P24627 |
| B | C-terminal peptide from lactotransferrin | protein | 6 | 0% helix, 0% strand | P24627 |
Ligands and binding sites
- XXD · (2S)-pentane-1,2,5-triol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · 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 | 236 | 0.73 | 0.88 | 39 | empty |
| 2 | 52 | 0.36 | 0.80 | 18 | empty |
| 3 | 71 | 0.34 | 0.76 | 12 | empty |
| 4 | 78 | 0.34 | 0.75 | 16 | empty |
| 5 | 73 | 0.30 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 270 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3UK4 · Crystal Structure of C-lobe of Bovine lactoferrin Complexed with 1,2,5-Pentanetriol at… · 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 3UK4 · PDBe 3UK4 · UniProt P24627
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