3T6I | pdb_00003t6i

Endothiapepsin in complex with an azepin derivative

• PDB DOI: https://doi.org/10.2210/pdb3T6I/pdb

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


• Deposited: 2011-07-28 Released: 2012-08-01 
• Deposition Author(s): Koester, H., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.149 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

Literature

Endothiapepsin in complex with an azepin derivative

Koester, H., Heine, A., Diederich, W.E., 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: 35.37 kDa 
• Atom Count: 2,903 
• 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NC8	B [auth A]	(3R)-3-({(4-aminobenzyl)[(4-aminophenyl)acetyl]amino}methyl)-5-{[(4-bromobenzoyl)oxy]methyl}-2,3,4,7-tetrahydro-1H-azepinium C30 H34 Br N4 O3 ILVATMQGTNYMLQ-XMMPIXPASA-O
NC9	C [auth A]	(3R)-3-({(4-aminobenzyl)[(4-aminophenyl)acetyl]amino}methyl)-5-(hydroxymethyl)-2,3,4,7-tetrahydro-1H-azepinium C23 H31 N4 O2 WRSLWDODYIRHLE-HXUWFJFHSA-O
Z82	D [auth A]	4-bromobenzoic acid C7 H5 Br O2 TUXYZHVUPGXXQG-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	G [auth A], H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.149 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.38	α = 90
b = 73.44	β = 109.96
c = 53.26	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Koester, H., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary