Research workbench
Ligand recognition in C-lobe: the crystal structure of the complex of lactoferrin C-lobe with nicotinamide at 2.5 a resolution
Analyse Ligand recognition in C-lobe: the crystal structure of the complex of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R9J
- 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
- NCA, NAG, ZN, FE, CO3, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin' (EC 3.4.21.-) | protein | 341 | 33% helix, 18% strand | P24627 |
Ligands and binding sites
- NCA · Nicotinamide · 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 · 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 | 270 | 0.74 | 0.87 | 40 | empty |
| 2 | 74 | 0.35 | 0.76 | 20 | NAG |
| 3 | 76 | 0.33 | 0.75 | 15 | empty |
| 4 | 53 | 0.31 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2R9J · Ligand recognition in C-lobe: The crystal structure of the complex of lactoferrin C-lobe… · 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 2R9J · PDBe 2R9J · UniProt P24627
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.