6AJ6 | pdb_00006aj6

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 (Depositor), 0.313 (DCC)
R-Value Work:
0.212 (Depositor), 0.228 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 826
Deposited Residue Count: 826
Unique protein chains: 1

Macromolecules

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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)) Explore Q387G0 Go to UniProtKB: Q387G0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	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] Interactions & Density 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 (Depositor), 0.313 (DCC)
R-Value Work: 0.212 (Depositor), 0.228 (DCC)
R-Value Observed: 0.216 (Depositor)

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

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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, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.