MolNFT v1 · #19413 · protein
Crystal structure of a complex of lactoferrin with a lanthanide ion (SM3+) at 3.4 ångström resolution
1QJM: “Crystal structure of a complex of lactoferrin with a lanthanide ion (SM3+) at 3.4 ångström resolution”. X-ray diffraction, 2 ligands (SM, CO3), 9 pockets (best druggability 0.77). MolNFT v1 #19413 on GenesisL1: 3D structure, binding…
- PDB
- 1QJM
- Type
- protein
- Length
- 689 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoferrin
- UniProt
- O77811
- Ligands
- SM, CO3
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoferrin | protein | 689 | 35% helix, 18% strand | O77811 |
Ligands and binding sites
- SM · Samarium (III) ion · metal · 2 copies · chains A
- CO3 · Carbonate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.77 | 0.92 | 37 | empty |
| 2 | 261 | 0.76 | 0.89 | 43 | empty |
| 3 | 310 | 0.68 | 0.82 | 35 | empty |
| 4 | 496 | 0.66 | 0.78 | 70 | empty |
| 5 | 139 | 0.46 | 0.77 | 21 | empty |
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 1QJM · Crystal Structure of a Complex of Lactoferrin with a Lanthanide Ion (SM3+) at 3.4… · the same entry in another collection · chain A against A, TM-score 1.00
- O77811 · AlphaFold monomer V2.0 prediction for lactotransferrin (O77811) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O77811
- Elsewhere: RCSB PDB 1QJM · PDBe 1QJM · UniProt O77811
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