6S7M | pdb_00006s7m

Structure of parasitic PEX14 in complex with a benzo[b]thiophene-7-carboxylic acid.

PDB DOI: https://doi.org/10.2210/pdb6S7M/pdb

Classification: SIGNALING PROTEIN
Organism(s): Trypanosoma brucei brucei
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-07-05 Released: 2020-07-15
Deposition Author(s): Hassaan, E., Heine, A., Klebe, G.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.267 (Depositor), 0.269 (DCC)
R-Value Work:
0.230 (Depositor), 0.234 (DCC)
R-Value Observed:
0.232 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure of parasitic PEX14 in complex with a benzo[b]thiophene-7-carboxylic acid.

Hassaan, E., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 63.89 kDa
Atom Count: 4,286
Modeled Residue Count: 524
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxin 14	A, B, C, D, E A, B, C, D, E, F, G, H	68	Trypanosoma brucei brucei	Mutation(s): 1 Gene Names: PEX14
UniProt
Find proteins for Q8IEW2 (Trypanosoma brucei brucei) Explore Q8IEW2 Go to UniProtKB: Q8IEW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IEW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KZ2 (Subject of Investigation/LOI) Query on KZ2 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain L [auth C] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain L [auth C] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain L [auth C]	I [auth A] K [auth B] L [auth C] M [auth D] O [auth E] I [auth A], K [auth B], L [auth C], M [auth D], O [auth E], P [auth E]	1-benzothiophene-7-carboxylic acid C₉ H₆ O₂ S LJPSRTWIAXVPIS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth D] mmCIF format, chain J [auth A] mmCIF format, chain N [auth D]	J [auth A], N [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth D] Interactions & Density Focus chain J [auth A] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.267 (Depositor), 0.269 (DCC)
R-Value Work: 0.230 (Depositor), 0.234 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.786	α = 90
b = 39.712	β = 90.082
c = 81.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Coot	model building
XDS	data scaling
XDS	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	Germany	--

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2024-05-15
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.