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Crystal structure of C-lobe of bovine lactoferrin complexed with gamma amino butyric acid at 1.44 a resolution
Analyse Crystal structure of C-lobe of bovine lactoferrin complexed with gamma amino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V5A
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin; C-terminal peptide of lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- ABU, NAG, ZN, FE, CO3
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 335 | 36% helix, 19% strand | P24627 |
| B | C-terminal peptide of lactotransferrin | protein | 6 | 0% helix, 0% strand | P24627 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · 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 · 2 copies · chains A
- GOL · Glycerol · additive · 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 | 257 | 0.72 | 0.86 | 40 | empty |
| 2 | 173 | 0.45 | 0.75 | 41 | NAG |
| 3 | 110 | 0.43 | 0.77 | 20 | empty |
| 4 | 61 | 0.31 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 291 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3V5A · Crystal Structure of C-lobe of Bovine Lactoferrin Complexed with Gamma Amino Butyric Acid… · 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 3V5A · PDBe 3V5A · UniProt P24627
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