Research workbench
Soluble rabbit neprilysin in complex with phosphoramidon
Analyse Soluble rabbit neprilysin in complex with phosphoramidon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZR5
- Type
- protein
- Length
- 1,392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neprilysin
- EC
- 3.4.24.11
- UniProt
- P08049
- Ligands
- RDF, NAG, ZN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neprilysin (EC 3.4.24.11) | protein | 696 | 58% helix, 8% strand | P08049 |
Ligands and binding sites
- RDF · N-alpha-L-rhamnopyranosyloxy(hydroxyphosphinyl)-L-leucyl-L-tryptophan · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.81 | 0.88 | 67 | empty |
| 2 | 713 | 0.73 | 0.79 | 89 | ZN, RDF |
| 3 | 198 | 0.66 | 0.85 | 38 | ZN, RDF |
| 4 | 531 | 0.66 | 0.77 | 62 | empty |
| 5 | 292 | 0.58 | 0.77 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 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 P08049
- Elsewhere: RCSB PDB 4ZR5 · PDBe 4ZR5 · UniProt P08049
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