MolNFT v1 · #49284 · protein
Crystal structure of the complex of bovine C-lobe with amygdalin at 2.3A resolution
2QJE · Lactotransferrin: “Crystal structure of the complex of bovine C-lobe with amygdalin at 2.3A resolution”. X-ray diffraction, 8 ligands (TVY, Z8T, NAG), 4 pockets (best druggability 0.74). MolNFT v1 #49284 on GenesisL1: 3D structure…
- PDB
- 2QJE
- Type
- protein
- Length
- 340 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- TVY, Z8T, NAG, BMA, ZN, FE, SO4, CO3
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 340 | 32% helix, 18% strand | P24627 |
Ligands and binding sites
- TVY · (1S)-2-amino-1-phenylethyl alpha-D-mannopyranoside · ligand · chains A
- Z8T · beta-L-glucopyranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- CO3 · Carbonate 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 | 244 | 0.74 | 0.88 | 39 | empty |
| 2 | 55 | 0.31 | 0.76 | 11 | empty |
| 3 | 57 | 0.30 | 0.75 | 11 | empty |
| 4 | 54 | 0.28 | 0.74 | 18 | NAG |
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2QJE · Crystal structure of the complex of Bovine C-lobe with Amygdalin at 2.3A resolution · 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 2QJE · PDBe 2QJE · UniProt P24627
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