Research workbench
Crystal structure of C-lobe of bovine lactoferrin complexed with N- acetylmuramyl L-alanyl D-isoglutamine at 1.8 a resolution
Analyse Crystal structure of C-lobe of bovine lactoferrin complexed with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DIG
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin; C-terminal peptide from lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- DGN, ALA, LAC, NAG, NDG, ZN, FE, CO3, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 335 | 35% helix, 19% strand | P24627 |
| B | C-terminal peptide from lactotransferrin | protein | 6 | 0% helix, 0% strand | P24627 |
Ligands and binding sites
- DGN · D-glutamine · ligand · chains A
- ALA · Alanine · ligand · chains A
- LAC · Lactic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- 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
- 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
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 | 202 | 0.72 | 0.89 | 39 | empty |
| 2 | 148 | 0.42 | 0.75 | 29 | NAG |
| 3 | 105 | 0.40 | 0.76 | 21 | empty |
| 4 | 68 | 0.33 | 0.75 | 10 | empty |
| 5 | 50 | 0.24 | 0.73 | 17 | NDG |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4DIG · Crystal Structure of C-lobe of Bovine lactoferrin Complexed with N-acetylmuramyl l-alanyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P24627 · AlphaFold monomer V2.0 prediction for lactotransferrin (P24627) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 4DIG · PDBe 4DIG · UniProt P24627
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