7ZVA

Crystal Structure of the native zymogen form of the glutamic-class prolyl-endopeptidase neprosin at 1.80 A resolution.

PDB DOI: https://doi.org/10.2210/pdb7ZVA/pdb

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

Deposited: 2022-05-14 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.218
R-Value Work: 0.182
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 44.79 kDa
Atom Count: 3,015
Modelled Residue Count: 335
Deposited Residue Count: 389
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal peptidase	A	389	Nepenthes ventricosa x Nepenthes alata	Mutation(s): 0
UniProt
Find proteins for A0A1L7NZU4 (Nepenthes alata) Explore A0A1L7NZU4 Go to UniProtKB: A0A1L7NZU4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L7NZU4
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

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	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A]	Q [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]