MolNFT v1 · #126177 · protein
Structure of human neurolysin (E475Q) in complex with amyloid-beta 35- 40 peptide product
5LV0 · Neurolysin, mitochondrial: “Structure of human neurolysin (E475Q) in complex with amyloid-beta 35- 40 peptide product”. X-ray diffraction, 2 ligands (ZN, CL), 20 pockets (best druggability 0.88). MolNFT v1 #126177 on GenesisL1: 3D…
- PDB
- 5LV0
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurolysin, mitochondrial; Gly-val-val amyloid 35-40 fragment
- EC
- 3.4.24.16
- UniProt
- Q9BYT8
- Ligands
- ZN, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurolysin, mitochondrial (EC 3.4.24.16) | protein | 666 | 59% helix, 8% strand | Q9BYT8 |
| B | Neurolysin, mitochondrial (EC 3.4.24.16) | protein | 663 | 60% helix, 7% strand | Q9BYT8 |
| C, D | Gly-val-val amyloid 35-40 fragment | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.88 | 0.90 | 82 | empty |
| 2 | 1146 | 0.87 | 0.88 | 103 | empty |
| 3 | 698 | 0.71 | 0.78 | 63 | empty |
| 4 | 197 | 0.66 | 0.85 | 28 | empty |
| 5 | 119 | 0.66 | 0.89 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 823 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 326 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 312 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5LV0 · Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYT8 · AlphaFold monomer V2.0 prediction for neurolysin, mitochondrial (Q9BYT8) · 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 Q9BYT8
- Elsewhere: RCSB PDB 5LV0 · PDBe 5LV0 · UniProt Q9BYT8
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