6AJC | pdb_00006ajc

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 (Depositor), 0.280 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (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

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.

Macromolecule Content

Total Structure Weight: 382.86 kDa
Atom Count: 26,905
Modeled Residue Count: 3,301
Deposited Residue Count: 3,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A, B, C, D, E 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4E4L7
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 AA [auth G] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] SDF format, chain DA [auth H] MOL2 format, chain AA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] MOL2 format, chain DA [auth H] mmCIF format, chain AA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F] mmCIF format, chain DA [auth H]	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		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
ICT Query on ICT Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] 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] SDF format, chain K [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] 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] MOL2 format, chain K [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain FA [auth H] 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] mmCIF format, chain K [auth A]	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		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [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 FA [auth H] Focus chain K [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]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain J [auth A] SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain BA [auth G]	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		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.283 (Depositor), 0.280 (DCC)
R-Value Work: 0.202 (Depositor), 0.206 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.765	α = 90
b = 123.485	β = 105.96
c = 127.04	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description