6S6R | pdb_00006s6r

First crystal structure of parasitic PEX14 in complex with a fragment molecule 1H-indole-7-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb6S6R/pdb

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

Deposited: 2019-07-03 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: 1.58 Å
R-Value Free:
0.235 (Depositor), 0.237 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

First crystal structure of parasitic PEX14 in complex with a fragment molecule 1H-indole-7-carboxylic acid

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

To be published.

Macromolecule Content

Total Structure Weight: 8.5 kDa
Atom Count: 634
Modeled Residue Count: 69
Deposited Residue Count: 69
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxin 14	A	69	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KXQ (Subject of Investigation/LOI) Query on KXQ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1~{H}-indole-7-carboxylic acid C₉ H₇ N O₂ IPDOBVFESNNYEE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.235 (Depositor), 0.237 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.306	α = 90
b = 43.306	β = 90
c = 80.942	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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Ligand Structure Quality Assessment

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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

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