7ZU8

Crystal Structure of the zymogen form of the glutamic-class prolyl-endopeptidase neprosin at 2.05 A resolution in presence of the crystallophore Lu-Xo4.

• PDB DOI: https://doi.org/10.2210/pdb7ZU8/pdb

• Classification: HYDROLASE
• Organism(s): Nepenthes ventricosa x Nepenthes alata
• Expression System: Homo sapiens neanderthalensis
• Mutation(s): No 


• Deposited: 2022-05-11 Released: 2022-08-10 
• Deposition Author(s): Del Amo-Maestro, L., Eckhard, U., Rodriguez-Banqueri, A., Mendes, S.R., Guevara, T., Gomis-Ruth, F.X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.27 kDa 
• Atom Count: 2,929 
• Modelled Residue Count: 336 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl endopeptidase Neprosin	A	389	Nepenthes ventricosa x Nepenthes alata	Mutation(s): 0  Gene Names: NvNpr EC: 3.4.21.19
UniProt
Find proteins for A0A1L7NZU4 (Nepenthes alata) Explore A0A1L7NZU4  Go to UniProtKB:  A0A1L7NZU4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K93	D [auth A], F [auth A]	12-oxidanyl-9,11$l^{3}-dioxa-1$l^{4},19$l^{4},22,27$l^{4},28$l^{4}-pentaza-10$l^{6}-lutetaoctacyclo[17.5.2.1^{3,7}.1^{10,13}.0^{1,10}.0^{10,19}.0^{10,28}.0^{17,27}]octacosa-3,5,7(28),11,13,15,17(27)-heptaen-8-one C20 H24 Lu N5 O4 ZJNYWMGNALTZQP-UHFFFAOYSA-M
ACT	E [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.65	α = 90
b = 93.35	β = 90
c = 48.69	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing
BUSTER	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Del Amo-Maestro, L., Eckhard, U., Rodriguez-Banqueri, A., Mendes, S.R., Guevara, T., Gomis-Ruth, F.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release