5OG7 | pdb_00005og7

Endothiapepsin in complex with hydrazide fragment

• PDB DOI: https://doi.org/10.2210/pdb5OG7/pdb

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


• Deposited: 2017-07-12 Released: 2018-08-08 
• Deposition Author(s): Metz, A., Klauser, P.C., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Endothiapepsin in complex with hydrazide fragment

Metz, A., Klauser, P.C., Rudek, M., Schmitz, B., Gohlke, H., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.16 kDa 
• Atom Count: 2,652 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLK	C [auth A]	3-chloranyl-~{N}'-(4,5-dihydro-1~{H}-imidazol-3-ium-2-yl)propanehydrazide C6 H12 Cl N4 O KIPZHINDKFZDKZ-UHFFFAOYSA-O
DMS	B [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.883	α = 90
b = 73.467	β = 109.4
c = 52.114	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Metz, A., Klauser, P.C., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary