5G4B | pdb_00005g4b

Crystal structure of Aura virus capsid protein in complex with piperazine.

PDB DOI: https://doi.org/10.2210/pdb5G4B/pdb

Classification: HYDROLASE
Organism(s): Aura virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-08 Released: 2016-07-20
Deposition Author(s): Aggarwal, M., Kumar, P., Tomar, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.265 (Depositor), 0.266 (DCC)
R-Value Work:
0.199 (Depositor), 0.202 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5G4B

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

Literature

Crystal Structure of Capsid Protein from Aura Virus in Complex with Piperazine

Aggarwal, M., Kumar, P., Tomar, S.

To be published.

Macromolecule Content

Total Structure Weight: 17.09 kDa
Atom Count: 1,226
Modeled Residue Count: 152
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN	A	158	Aura virus	Mutation(s): 0 EC: 3.4.21.90
UniProt
Find proteins for Q86925 (Aura virus) Explore Q86925 Go to UniProtKB: Q86925
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PZE Query on PZE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	piperazine C₄ H₁₀ N₂ GLUUGHFHXGJENI-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: 2.24 Å
R-Value Free: 0.265 (Depositor), 0.266 (DCC)
R-Value Work: 0.199 (Depositor), 0.202 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.256	α = 90
b = 34.839	β = 101.94
c = 49.169	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2017-03-29
Changes: Other
Version 1.2: 2017-07-05
Changes: Data collection
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.