8R3I | pdb_00008r3i

Proof of concept study of a probe molecule in TbPTR1

PDB DOI: https://doi.org/10.2210/pdb8R3I/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trypanosoma brucei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-11-09 Released: 2024-11-20
Deposition Author(s): Dawson, A., GIlbert, I.H., Montagna, S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.190 (Depositor), 0.198 (DCC)
R-Value Work:
0.165 (Depositor), 0.176 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Proof of concept study of a probe molecule in TbPTR1

Montagna, S., Gilbert, I.H., Dawson, A.

To be published.

Macromolecule Content

Total Structure Weight: 125.48 kDa
Atom Count: 8,320
Modeled Residue Count: 1,000
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pteridine reductase	A, B, C, D	282	Trypanosoma brucei	Mutation(s): 0 Gene Names: PTR1
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei) Explore O76290 Go to UniProtKB: O76290
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O76290
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], I [auth C], L [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
XSH (Subject of Investigation/LOI) Query on XSH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth B], K [auth C], M [auth D]	~{N}-[(2~{R})-1-[4-[[2,4-bis(azanyl)quinazolin-5-yl]oxymethyl]piperidin-1-yl]-1-oxidanylidene-pent-4-yn-2-yl]ethanamide C₂₁ H₂₆ N₆ O₃ KEUMDTOQJJKEPR-MRXNPFEDSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]