9C5M | pdb_00009c5m

Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH structure in complex with NADH and malonate (P1 space group)

PDB DOI: https://doi.org/10.2210/pdb9C5M/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: 1.69 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.148 (Depositor), 0.149 (DCC)
R-Value Observed:
0.148 (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: 235.39 kDa
Atom Count: 18,365
Modeled Residue Count: 2,106
Deposited Residue Count: 2,160
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, E A, B, C, D, E, F, G, H	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain FA [auth G] SDF format, chain HA [auth H] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] FA [auth G] HA [auth H] M [auth A] P [auth B] BA [auth F], FA [auth G], HA [auth H], M [auth A], P [auth B], S [auth C], V [auth D], Y [auth E]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	CA [auth G] GA [auth H] I [auth A] N [auth B] Q [auth C] CA [auth G], GA [auth H], I [auth A], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	AA [auth F] DA [auth G] EA [auth G] J [auth A] K [auth A] AA [auth F], DA [auth G], EA [auth G], J [auth A], K [auth A], L [auth A], O [auth B], R [auth C], U [auth D], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]