MolNFT v1 · #34718 · protein
Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with adenosine at 2.4 a resolution
2DOJ · Lactotransferrin: “Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with adenosine at 2.4 a resolution”. X-ray diffraction, 9 ligands (ADN, NAG, BMA), 5 pockets (best druggability 0.73). MolNFT v1 #34718 on…
- PDB
- 2DOJ
- 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
- ADN, NAG, BMA, MAN, NDG, ZN, FE, SO4, CO3
- Pockets
- 5 · best druggability 0.73
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 | 341 | 32% helix, 18% strand | P24627 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 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
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 | 263 | 0.73 | 0.87 | 38 | empty |
| 2 | 60 | 0.32 | 0.76 | 11 | empty |
| 3 | 61 | 0.29 | 0.74 | 12 | empty |
| 4 | 65 | 0.28 | 0.73 | 19 | ADN |
| 5 | 60 | 0.26 | 0.72 | 16 | NAG |
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2DOJ · Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with adenosine… · 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 2DOJ · PDBe 2DOJ · UniProt P24627
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