MolNFT v1 · #82138 · protein
Crystal structure of C-lobe of bovine lactoferrin complexed with diaminopimelic acid at 1.46 a resolution
3VDF · Lactotransferrin: “Crystal structure of C-lobe of bovine lactoferrin complexed with diaminopimelic acid at 1.46 a resolution”. X-ray diffraction, 6 ligands (API, NAG, ZN), 4 pockets (best druggability 0.72). MolNFT v1 #82138 on…
- PDB
- 3VDF
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin; C-terminal peptide of lactotransferrin
- EC
- 3.4.21.-
- UniProt
- P24627
- Ligands
- API, NAG, ZN, FE, CO3, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactotransferrin (EC 3.4.21.-) | protein | 335 | 36% helix, 19% strand | P24627 |
| B | C-terminal peptide of lactotransferrin | protein | 6 | 0% helix, 0% strand | P24627 |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · 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 | 236 | 0.72 | 0.87 | 40 | empty |
| 2 | 170 | 0.45 | 0.75 | 40 | NAG |
| 3 | 96 | 0.40 | 0.77 | 20 | empty |
| 4 | 59 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 240 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3VDF · Crystal Structure of C-lobe of Bovine lactoferrin Complexed with diaminopimelic acid at… · 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 3VDF · PDBe 3VDF · UniProt P24627
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