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Crystal Structure of C-lobe of Bovine lactoferrin Complexed with Imidazol (1,2 a) pyridine3-yl-acitic acid at 2.4 A Resolution
Analyse Crystal Structure of C-lobe of Bovine lactoferrin Complexed with Imidazol (1,2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3USD
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Bos taurus
- Molecule
- Lactotransferrin; C-terminal peptide of Lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- IDL, NAG, BMA, ZN, FE, CO3, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 335 | 33% helix, 19% strand | P24627 |
| B | C-terminal peptide of Lactotransferrin | protein | 6 | 0% helix, 0% strand | P24627 |
Ligands and binding sites
- IDL · imidazo[1,2-a]pyridin-3-ylacetic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.73 | 0.89 | 43 | empty |
| 2 | 54 | 0.30 | 0.76 | 13 | empty |
| 3 | 66 | 0.29 | 0.74 | 18 | empty |
| 4 | 53 | 0.29 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3USD · Crystal structure of C-lobe of bovine lactoferrin complexed with imidazol (1,2 a)… · the same entry in another collection · chain A against A, TM-score 1.00
- P24627 · AlphaFold monomer V2.0 prediction for lactotransferrin (P24627) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 3USD · PDBe 3USD · UniProt P24627
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