7QOZ | pdb_00007qoz

Crystal structure of NAD-bound glycosomal malate dehydrogenase from Trypanosoma cruzi

PDB DOI: https://doi.org/10.2210/pdb7QOZ/pdb

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

Deposited: 2021-12-30 Released: 2023-07-12
Deposition Author(s): Sonani, R.R., Dubin, G.
Funding Organization(s): Polish National Science Centre, Foundation for Polish Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.208 (Depositor), 0.212 (DCC)
R-Value Work:
0.174 (Depositor), 0.181 (DCC)
R-Value Observed:
0.176 (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 NAD-bound glycosomal malate dehydrogenase from Trypanosoma cruzi

Sonani, R.R., Dubin, G.

To be published.

Macromolecule Content

Total Structure Weight: 287.06 kDa
Atom Count: 20,724
Modeled Residue Count: 2,582
Deposited Residue Count: 2,648
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	331	Trypanosoma cruzi	Mutation(s): 0 Gene Names: C3747_2g261, ECC02_003170 EC: 1.1.1.37
UniProt
Find proteins for A0A2V2XLH9 (Trypanosoma cruzi) Explore A0A2V2XLH9 Go to UniProtKB: A0A2V2XLH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2V2XLH9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain S [auth E] SDF format, chain R [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D]	I [auth A] L [auth B] N [auth C] R [auth D] S [auth E] I [auth A], L [auth B], N [auth C], R [auth D], S [auth E], T [auth F], V [auth G], W [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth H]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth F]	J [auth A] K [auth A] M [auth B] O [auth C] P [auth C] J [auth A], K [auth A], M [auth B], O [auth C], P [auth C], Q [auth C], U [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth F]