3Q6Y

Endothiapepsin in complex with a pyrrolidine based inhibitor

PDB DOI: https://doi.org/10.2210/pdb3Q6Y/pdb

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

Deposited: 2011-01-04 Released: 2012-01-04
Deposition Author(s): Koester, H., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.184
R-Value Work: 0.166
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Endothiapepsin in complex with a pyrrolidine based inhibitor

Koester, H., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 34.75 kDa
Atom Count: 2,572
Modelled Residue Count: 305
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S47 Query on S47 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(3S,4S)-pyrrolidine-3,4-diyl bis(naphthalen-1-ylacetate) C₂₈ H₂₅ N O₄ ATWKPWWBTFNYMB-UIOOFZCWSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
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: 1.35 Å
R-Value Free: 0.184
R-Value Work: 0.166
R-Value Observed: 0.167
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.36	α = 90
b = 72.79	β = 108.6
c = 51.79	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-04

Deposition Author(s):

Koester, H.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2012-01-04
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3Q6Y

Endothiapepsin in complex with a pyrrolidine based inhibitor

Endothiapepsin in complex with a pyrrolidine based inhibitor

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)