9C5K | pdb_00009c5k

Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH structure in complex with NADPH and malonate

PDB DOI: https://doi.org/10.2210/pdb9C5K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-06-06 Released: 2025-08-27
Deposition Author(s): Hashimoto, H., Debler, E.W.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.168 (Depositor), 0.168 (DCC)
R-Value Work:
0.138 (Depositor), 0.139 (DCC)
R-Value Observed:
0.139 (Depositor)

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

Trypanosoma cruzi D-3-hydroxybutyrate dehydrogenase (HBDH) is NADP-dependent enzyme.

Hashimoto, H., Debler, E.W.

To be published.

Macromolecule Content

Total Structure Weight: 119 kDa
Atom Count: 8,952
Modeled Residue Count: 1,049
Deposited Residue Count: 1,080
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxybutyrate dehydrogenase	A, B, C, D	270	Trypanosoma cruzi	Mutation(s): 3 Gene Names: C4B63_13g310 EC: 1.1.1.100
UniProt
Find proteins for A0A2V2VPF1 (Trypanosoma cruzi) Explore A0A2V2VPF1 Go to UniProtKB: A0A2V2VPF1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2V2VPF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain R [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], R [auth C], Y [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain Y [auth D]
MLI (Subject of Investigation/LOI) Query on MLI Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain N [auth B]	H [auth A], N [auth B], V [auth C], Z [auth D]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain V [auth C] Focus chain Z [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] I [auth A] J [auth A] O [auth B] AA [auth D], BA [auth D], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], W [auth C], X [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B], M [auth B], S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain G [auth A] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain G [auth A] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain G [auth A]	G [auth A], T [auth C], U [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain T [auth C] Focus chain U [auth C]