1E80 | pdb_00001e80

Endothiapepsin complex with renin inhibitor MERCK-KGAA-EMD56133

• PDB DOI: https://doi.org/10.2210/pdb1E80/pdb

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


• Deposited: 2000-09-15 Released: 2000-09-26 
• Deposition Author(s): Read, J.A., Cooper, J.B., Toldo, L., Rippmann, F., Raddatz, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.221 (Depositor) 
• R-Value Work: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Refinement of Four Endothiapepsin Inhibitor Complexes. Crystallographic Studies of Cytochrome Ch from Methylobacterium Extorquens and Inhibitor Complexes of Aspartic Proteinases.

Read, J.A.

(1999) Ph D Thesis 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA 1.14 (software)

Macromolecule Content 

• Total Structure Weight: 34.61 kDa 
• Atom Count: 2,612 
• 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 [auth E]	330	Cryphonectria parasitica	Mutation(s): 0  EC: 3.4.23.23 (PDB Primary Data), 3.4.23.22 (UniProt)
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838  Go to UniProtKB:  P11838

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0GQ	B [auth E]	4-amino-N-{(1R,8R,9R,13R)-16-(4-amino-2-methylpyrimidin-5-yl)-1-benzyl-8-(cyclohexylmethyl)-9-hydroxy-13-[(1S)-1-methylpropyl]-2,6,11,14-tetraoxo-3,7,12,15-tetraazahexadec-1-yl}piperidine-1-carboxamide C41 H64 N10 O6 HZSPXNCSLJOMIF-NQKKVWJDSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000296 (0GQ)	B [auth E]	MERCK-KGAA-EMD56133	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.221 (Depositor) 
• R-Value Work:  0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.21	α = 90
b = 74.71	β = 109.46
c = 46.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-09-26 
Deposition Author(s): Read, J.A., Cooper, J.B., Toldo, L., Rippmann, F., Raddatz, P.

Revision History  

• Version 1.0: 2000-09-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary