4W5B | pdb_00004w5b

Crystal structure analysis of cruzain with Fragment 1 (N-(1H-benzimidazol-2-yl)-1,3-dimethyl-pyrazole-4-carboxamide)

PDB DOI: https://doi.org/10.2210/pdb4W5B/pdb

Classification: HYDROLASE/HYDROLASE Inhibitor
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-08-17 Released: 2015-03-04
Deposition Author(s): Tochowicz, A., McKerrow, J.H., Craik, C.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.212 (Depositor), 0.216 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Applying Fragments Based- Drug Design to identify multiple binding modes on cysteine protease.

Tochowicz, A., Lee, G.M., Arkin, M.R., Neitz, J., McKerrow, J.H., Craik, C.S.

To be published.

Macromolecule Content

Total Structure Weight: 68.86 kDa
Atom Count: 4,927
Modeled Residue Count: 645
Deposited Residue Count: 645
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cruzipain	A, B, C	215	Trypanosoma cruzi	Mutation(s): 1 EC: 3.4.22.51
UniProt
Find proteins for P25779 (Trypanosoma cruzi) Explore P25779 Go to UniProtKB: P25779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3H5 Query on 3H5 Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide C₁₃ H₁₃ N₅ O ATWRDFSNOOXDOA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.254 (Depositor), 0.255 (DCC)
R-Value Work: 0.212 (Depositor), 0.216 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.1	α = 90
b = 137.1	β = 90
c = 109.8	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description, Source and taxonomy
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.