MolNFT v1 · #67118 · protein
Structural basis of the prevention of nsaid-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: binding and structural studies of C- lobe complex with diclofenac
3IB0 · Lactotransferrin: “Structural basis of the prevention of nsaid-induced damage of the gastrointestinal tract by C-terminal half…”. X-ray diffraction, 7 ligands (DIF, MAN, NAG), 5 pockets (best druggability 0.74). MolNFT v1 #67118 on…
- PDB
- 3IB0
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- DIF, MAN, NAG, ZN, FE, SO4, CO3
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 341 | 35% helix, 18% strand | P24627 |
Ligands and binding sites
- DIF · 2-[2,6-dichlorophenyl)amino]benzeneacetic acid · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CO3 · Carbonate ion · ion · chains A
- EOH · Ethanol · additive · 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 | 237 | 0.74 | 0.88 | 39 | empty |
| 2 | 129 | 0.44 | 0.77 | 36 | NAG |
| 3 | 107 | 0.36 | 0.74 | 34 | DIF |
| 4 | 64 | 0.32 | 0.75 | 11 | empty |
| 5 | 55 | 0.28 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3IB0 · Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract… · 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 3IB0 · PDBe 3IB0 · UniProt P24627
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