6AJ6

Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+

PDB DOI: https://doi.org/10.2210/pdb6AJ6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trypanosoma brucei brucei
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: 3.20 Å
R-Value Free: 0.309
R-Value Work: 0.212
R-Value Observed: 0.216

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: 95.07 kDa
Atom Count: 6,660
Modelled Residue Count: 826
Deposited Residue Count: 826
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A, B [auth C]	413	Trypanosoma brucei brucei	Mutation(s): 1 EC: 1.1.1.42
UniProt
Find proteins for Q387G0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Go to UniProtKB: Q387G0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth C] MOL2 format, chain C [auth A] MOL2 format, chain D [auth C] mmCIF format, chain C [auth A] mmCIF format, chain D [auth C]	C [auth A], D [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.309
R-Value Work: 0.212
R-Value Observed: 0.216
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.442	α = 90
b = 109.754	β = 89.98
c = 64.961	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.