5QB6 | pdb_00005qb6

Crystal structure of Endothiapepsin-FRG062 complex

• PDB DOI: https://doi.org/10.2210/pdb5QB6/pdb
• Deposition Group: G_1002039 ExploreG_1002039

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


• Deposited: 2017-08-04 Released: 2020-04-22 
• Deposition Author(s): Huschmann, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Literature

Crystal structure of Endothiapepsin

Huschmann, F.U., Weiss, M.S., Mueller, U., Haustedt, L.O., Klebe, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.62 kDa 
• Atom Count: 2,820 
• Modeled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D5Y	H [auth A]	methyl 3-(5-bromo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alaninate C8 H10 Br N3 O4 SWCNOWRHWSFLMA-YFKPBYRVSA-N
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.345	α = 90
b = 73.317	β = 109.55
c = 52.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Huschmann, F.

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2021-11-17
  Changes: Advisory, Database references, Structure summary
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary