MolNFT v1 · #61691 · protein
Engineered human lipocalin 2 in complex with Y-dtpa
3DSZ: “Engineered human lipocalin 2 in complex with Y-dtpa”. X-ray diffraction, 2 ligands (LIZ, YT3), 4 pockets (best druggability 0.73). MolNFT v1 #61691 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DSZ
- Type
- protein
- Length
- 345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engineered human lipocalin 2
- Ligands
- LIZ, YT3
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Engineered human lipocalin 2 | protein | 172 | 15% helix, 44% strand | — |
| B | Engineered human lipocalin 2 | protein | 173 | 17% helix, 43% strand | — |
Ligands and binding sites
- LIZ · N-{(1S,2S)-2-[bis(carboxymethyl)amino]cyclohexyl}-N-{(2R)-2-[bis(carboxymethyl)amino]-3-[4-({[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]carbamothioyl}amino)phenyl]propyl}glycine · ligand · 2 copies · chains A, B
- YT3 · Yttrium (III) ion · metal · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.73 | 0.79 | 51 | LIZ, YT3 |
| 2 | 641 | 0.68 | 0.77 | 49 | LIZ, YT3 |
| 3 | 182 | 0.47 | 0.76 | 25 | empty |
| 4 | 87 | 0.36 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 333 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3DSZ · Engineered human lipocalin 2 in complex with Y-DTPA · 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
- Elsewhere: RCSB PDB 3DSZ · PDBe 3DSZ
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