Research workbench
Crystal structure of an engineered lipocalin (anticalin H1GA) in complex with the alzheimer amyloid peptide ABETA1-40
Analyse Crystal structure of an engineered lipocalin (anticalin H1GA) 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
- 4MVL
- Type
- protein
- Length
- 730 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin; Beta-amyloid protein 40
- UniProt
- P80188, P05067
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 173 | 13% helix, 40% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 172 | 11% helix, 40% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 11% helix, 37% strand | P80188 |
| D | Neutrophil gelatinase-associated lipocalin | protein | 171 | 12% helix, 40% strand | P80188 |
| E, F | Beta-amyloid protein 40 | protein | 11 | 0% helix, 0% strand | P05067 |
| G, H | Beta-amyloid protein 40 | protein | 9 | 0% helix, 0% strand | P05067 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.76 | 0.78 | 111 | empty |
| 2 | 226 | 0.62 | 0.82 | 26 | empty |
| 3 | 227 | 0.60 | 0.80 | 28 | empty |
| 4 | 200 | 0.59 | 0.81 | 30 | empty |
| 5 | 163 | 0.53 | 0.79 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–E · 809 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 714 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 685 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 669 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4MVL · Crystal structure of an engineered lipocalin (Anticalin H1GA) in complex with the… · the same entry in another collection · chain H against H, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain F 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 4MVL · PDBe 4MVL · UniProt P80188 · UniProt P05067
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