Research workbench
Crystal structure of an engineered lipocalin (anticalin US7) in complex with the alzheimer amyloid peptide fragment vffaed
Analyse Crystal structure of an engineered lipocalin (anticalin US7) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MVK
- Type
- protein
- Length
- 177 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin; Amyloid peptide fragment vffaed
- UniProt
- P80188, P05067
- Ligands
- ACE, NH2
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 171 | 13% helix, 42% strand | P80188 |
| B | Amyloid peptide fragment vffaed | protein | 6 | 0% helix, 0% strand | P05067 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.51 | 0.81 | 25 | NH2 |
Interfaces
1 interface between chains.
- A–B · 603 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 4MVK · Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain B against A, TM-score 0.34
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 P80188
- Every structure of UniProt P05067
- Elsewhere: RCSB PDB 4MVK · PDBe 4MVK · UniProt P80188 · UniProt P05067
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