7NKW

Endothiapepsin structure obtained at 298K after a soaking with fragment JFD03909 from a dataset collected with JUNGFRAU detector

PDB DOI: https://doi.org/10.2210/pdb7NKW/pdb

Classification: HYDROLASE
Organism(s): Cryphonectria parasitica
Mutation(s): No

Deposited: 2021-02-19 Released: 2022-03-02
Deposition Author(s): Engilberge, S., Huang, C.-Y., Leonarski, F., Wojdyla, J.A., Marsh, M., Olieric, V., Wang, M.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.227
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

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

Literature

Endothiapepsin structure obtained at 298K after a soaking with fragment JFD03909 from a dataset collected with JUNGFRAU detector

Engilberge, S., Huang, C.-Y., Smith, K.M.L., Eris, D., Wojdyla, J.A., Olieric, V., Leonarski, F., Sharpe, M., Wang, M.

To be published.

Macromolecule Content

Total Structure Weight: 33.89 kDa
Atom Count: 2,468
Modelled Residue Count: 326
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	330	Cryphonectria parasitica	Mutation(s): 0 EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838 Go to UniProtKB: P11838
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11838
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.227
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.005	α = 90
b = 74.636	β = 108.39
c = 52.826	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	200021_182369

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.