6AJC

Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with NADP+, isocitrate and ca2+

PDB DOI: https://doi.org/10.2210/pdb6AJC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-08-27 Released: 2019-08-28
Deposition Author(s): Wang, X., Inaoka, D.K., Shiba, T., Balogun, E.O., Ziebart, N., Allman, S., Watanabe, Y., Nozaki, T., Boshart, M., Bringaud, F., Harada, S., Kita, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.283
R-Value Work: 0.202
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+)

Wang, X., Inaoka, D.K., Shiba, T., Balogun, E.O., Ziebart, N., Allman, S., Watanabe, Y., Nozaki, T., Boshart, M., Bringaud, F., Harada, S., Kita, K.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A, B, C, D, E, F, G, H A, B, C, D, E, F, G, H	413	Trypanosoma cruzi strain CL Brener	Mutation(s): 1 Gene Names: Tc00.1047053506925.319 EC: 1.1.1.42
UniProt
Find proteins for Q4E4L7 (Trypanosoma cruzi (strain CL Brener)) Explore Q4E4L7 Go to UniProtKB: Q4E4L7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4E4L7
Protein Feature View 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 O [auth C] SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain O [auth C] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F]	AA [auth G], DA [auth H], I [auth A], L [auth B], O [auth C], AA [auth G], DA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction
ICT Query on ICT Download Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain Z [auth F]	CA [auth G], FA [auth H], K [auth A], N [auth B], Q [auth C], CA [auth G], FA [auth H], K [auth A], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	ISOCITRIC ACID C₆ H₈ O₇ ODBLHEXUDAPZAU-ZAFYKAAXSA-N		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain BA [auth G] SDF format, chain EA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain S [auth D] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F]	BA [auth G], EA [auth H], J [auth A], M [auth B], P [auth C], BA [auth G], EA [auth H], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction