5MB0 | pdb_00005mb0

Cocktail experiment A: fragments 63, 267, and 291 in complex with Endothiapepsin

• PDB DOI: https://doi.org/10.2210/pdb5MB0/pdb

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


• Deposited: 2016-11-07 Released: 2017-12-20 
• Deposition Author(s): Radeva, N., Heine, A., Klebe, G.
• Funding Organization(s): BMBF

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.151 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

Comparison of cocktail versus single soaking experimets

Radeva, N., 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: 35.28 kDa 
• Atom Count: 2,920 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F91	J [auth A], K [auth A]	N-(pyridin-4-ylmethyl)-2,3-dihydro-1,4-benzodioxin-6-amine C14 H14 N2 O2 ZEHRBOVXNPCYAK-UHFFFAOYSA-N
47V	I [auth A]	2,5-dimethyl-N-(pyridin-4-yl)furan-3-carboxamide C12 H12 N2 O2 LSWLYNGTJMNMRF-UHFFFAOYSA-N
F63	L [auth A]	N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine C11 H12 N2 O2 MUKCVLFJCGZPKF-UHFFFAOYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	B [auth A], C [auth A], D [auth A], 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: 1.15 Å
• R-Value Free:  0.151 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.377	α = 90
b = 73.079	β = 109.59
c = 52.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XSCALE	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Radeva, N., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
BMBF	Germany	05K13RM1

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary