5MB7

Cocktail experiment B: fragments 224 and 236 at 50mM concentration

PDB DOI: https://doi.org/10.2210/pdb5MB7/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.150
R-Value Work: 0.129
R-Value Observed: 0.130

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Comparison of cocktail versus single soaking experiments

Radeva, N., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 34.11 kDa
Atom Count: 2,774
Modelled Residue Count: 330
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11838
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4AV Query on 4AV Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1-(2-chloro-5-nitrophenyl)-N-methylmethanamine C₈ H₉ Cl N₂ O₂ YRTNCUPHKWUHMQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.150
R-Value Work: 0.129
R-Value Observed: 0.130
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.398	α = 90
b = 72.858	β = 109.46
c = 52.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XSCALE	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
BMBF	Germany	05K13RM1

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.