MolNFT v1 · #62246 · protein
Crystal structure of the complex of C-lobe of lactoferrin with nimesulide at 2.7 a resolution
3E9X · Lactotransferrin': “Crystal structure of the complex of C-lobe of lactoferrin with nimesulide at 2.7 a resolution”. X-ray diffraction, 7 ligands (NIM, NAG, MAN), 5 pockets (best druggability 0.74). MolNFT v1 #62246 on GenesisL1: 3D…
- PDB
- 3E9X
- 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
- NIM, NAG, MAN, ZN, FE, CO3, SO4
- Pockets
- 5 · 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
- NIM · 4-nitro-2-phenoxymethanesulfonanilide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 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
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 | 264 | 0.74 | 0.87 | 39 | empty |
| 2 | 111 | 0.40 | 0.76 | 19 | empty |
| 3 | 113 | 0.37 | 0.74 | 29 | NAG |
| 4 | 63 | 0.33 | 0.76 | 13 | empty |
| 5 | 64 | 0.31 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3E9X · Crystal Structure of the Complex of C-lobe of Lactoferrin with Nimesulide at 2.7 A… · 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 3E9X · PDBe 3E9X · UniProt P24627
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