7S1D | pdb_00007s1d

Crystal structure of E.coli DsbA in complex with compound MIPS-0001877 (compound 39)

PDB DOI: https://doi.org/10.2210/pdb7S1D/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-09-02 Released: 2023-02-08
Deposition Author(s): Heras, B., Scanlon, M.J., Martin, J.L., Caria, S.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7S1D

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Fluoromethylketone-fragment conjugates designed as covalent modifiers of EcDsbA are atypical substrates

Bradley, C.D., Whitehouse, R.L., Rimmer, K., Williams, M., Heras, B., Caria, S., Ilyichova, O., Vazirani, M., Mohanty, B., Harper, J., Scanlon, M.J., Simpson, J.S.

(2022) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2022-262lh

Macromolecule Content

Total Structure Weight: 42.71 kDa
Atom Count: 3,504
Modeled Residue Count: 376
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbA	A, B	189	Escherichia coli K-12	Mutation(s): 0 Gene Names: dsbA, dsf, ppfA, b3860, JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4 Go to UniProtKB: P0AEG4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
648 (Subject of Investigation/LOI) Query on 648 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-[3-(thiophen-3-yl)benzyl]piperidin-2-one C₁₆ H₁₇ N O S UMRKGGGHCYSVML-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.194 (Depositor), 0.195 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.966	α = 90
b = 64.22	β = 126.04
c = 74.356	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT455860

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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.