6ORU | pdb_00006oru

Crystal structure of Bira from S. aureus in complex with a acylsulfamide analogue of biotinyl-5'-AMP

PDB DOI: https://doi.org/10.2210/pdb6ORU/pdb

Classification: LIGASE/INHIBITOR
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-01 Released: 2020-07-01
Deposition Author(s): Wilce, M.C.J., Cini, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.187 (Depositor), 0.191 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Enhancing the stability of the sulfonamide linker of BPL inhibitors

Lee, K.J., Abell, A.D.

To be published.

Macromolecule Content

Total Structure Weight: 38.53 kDa
Atom Count: 2,662
Modeled Residue Count: 322
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional ligase/repressor BirA	A	329	Staphylococcus aureus	Mutation(s): 0 Gene Names: birA, M1K003_0300 EC: 6.3.4.15
UniProt
Find proteins for A0A3A5LBF0 (Staphylococcus aureus) Explore A0A3A5LBF0 Go to UniProtKB: A0A3A5LBF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3A5LBF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N3G (Subject of Investigation/LOI) Query on N3G 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]	N-{[4-(6-amino-9H-purin-9-yl)butyl]sulfamoyl}-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide C₁₉ H₂₉ N₉ O₄ S₂ WPCYKZJXLXIRGW-YDHLFZDLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.227 (Depositor), 0.230 (DCC)
R-Value Work: 0.187 (Depositor), 0.191 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.54	α = 90
b = 92.54	β = 90
c = 128.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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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.