Research workbench
High resolution crystal structure of substrate-free human neprilysin
Analyse High resolution crystal structure of substrate-free human neprilysin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GID
- 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
- NAG, ZN, NO3, PO4
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neprilysin (EC 3.4.24.11) | protein | 696 | 59% helix, 8% strand | P08473 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- NO3 · Nitrate ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
- GOL · Glycerol · additive · 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 | 159 | 0.66 | 0.87 | 37 | PEG, PO4 |
| 2 | 489 | 0.65 | 0.77 | 63 | EDO |
| 3 | 350 | 0.60 | 0.77 | 45 | NO3, PEG |
| 4 | 74 | 0.49 | 0.84 | 20 | empty |
| 5 | 127 | 0.47 | 0.78 | 24 | empty |
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 6GID · PDBe 6GID · UniProt P08473
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