5OML | pdb_00005oml

Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules to investigate the water envelope

PDB DOI: https://doi.org/10.2210/pdb5OML/pdb

Classification: SIGNALING PROTEIN
Organism(s): Trypanosoma brucei brucei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-01 Released: 2019-03-06
Deposition Author(s): Ratkova, E.L., Dawidowski, M., Napolitano, V., Dubin, G., Fino, R., Popowicz, G., Sattler, M., Tetko, I.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.202 (Depositor), 0.181 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules to investigate the water envelope

Ratkova, E.L., Dawidowski, M., Napolitano, V., Dubin, G., Fino, R., Popowicz, G., Sattler, M., Tetko, I.V.

To be published.

Macromolecule Content

Total Structure Weight: 33.93 kDa
Atom Count: 2,799
Modeled Residue Count: 261
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxin 14	A, B, C, D	67	Trypanosoma brucei brucei	Mutation(s): 0 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9YB (Subject of Investigation/LOI) Query on 9YB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], I [auth B], L [auth C], P [auth D]	(3~{R})-3-[[1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]carbonylamino]-3-phenyl-propanoic acid C₃₀ H₃₂ N₄ O₅ FEINFPMXJVPOSJ-RUZDIDTESA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	F [auth A], G [auth A], J [auth B], M [auth C], N [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain H [auth A]	H [auth A], K [auth B], O [auth C], Q [auth D]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain Q [auth D]