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Soluble rabbit neprilysin in complex with thiorphan

Analyse Soluble rabbit neprilysin in complex with thiorphan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5V48
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: TIO, NAG, ZN
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Neprilysin (EC 3.4.24.11)	protein	696	56% helix, 8% strand	P08049

Ligands and binding sites

TIO · (2-mercaptomethyl-3-phenyl-propionyl)-glycine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 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

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	758	0.83	0.86	96	empty
2	627	0.72	0.80	84	TIO
3	659	0.72	0.79	85	TIO
4	298	0.59	0.78	40	empty
5	295	0.57	0.77	39	empty

Interfaces

1 interface between chains.

A–B · 1063 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

5V48 · Soluble rabbit neprilysin in complex with thiorphan · the same entry in another collection · chain A against A, TM-score 1.00
P08049 · AlphaFold monomer V2.0 prediction for neprilysin (P08049) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 5V48 · PDBe 5V48 · UniProt P08049

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