Research workbench
Crystal structure of neprilysin in complex with sampatrilat.
Analyse Crystal structure of neprilysin in complex with sampatrilat. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XVP
- Type
- protein
- Length
- 696 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neprilysin
- EC
- 3.4.24.11
- UniProt
- P08473
- Ligands
- D0Z, NAG, ZN
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neprilysin (EC 3.4.24.11) | protein | 696 | 59% helix, 7% strand | P08473 |
Ligands and binding sites
- D0Z · Sampatrilat · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.67 | 0.87 | 37 | ZN, D0Z |
| 2 | 423 | 0.67 | 0.79 | 70 | EDO |
| 3 | 81 | 0.55 | 0.86 | 19 | empty |
| 4 | 168 | 0.47 | 0.76 | 26 | empty |
| 5 | 122 | 0.46 | 0.79 | 20 | EDO |
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 P08473
- Elsewhere: RCSB PDB 6XVP · PDBe 6XVP · UniProt P08473
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