1HEX

STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH NAD+: LIGAND-INDUCED LOOP-CLOSING AND MECHANISM FOR COFACTOR SPECIFICITY

PDB DOI: https://doi.org/10.2210/pdb1HEX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1994-09-09 Released: 1994-12-20
Deposition Author(s): Hurley, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Work: 0.182
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of 3-isopropylmalate dehydrogenase in complex with NAD+: ligand-induced loop closing and mechanism for cofactor specificity.

Hurley, J.H., Dean, A.M.

(1994) Structure 2: 1007-1016

PubMed: 7881901 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(94)00104-9
Primary Citation of Related Structures:
1HEX

PubMed Abstract:
The leucine biosynthetic enzyme 3-isopropylmalate dehydrogenase (IMDH) belongs to a unique class of bifunctional decarboxylating dehydrogenases. The two best-known members of this family, IMDH and isocitrate dehydrogenase (IDH), share a common structural framework and catalytic mechanism but have different substrate and cofactor specificities. IMDH is NAD(+)-dependent, while IDHs occur in both NAD(+)-dependent and NADP(+)-dependent forms.

Organizational Affiliation

Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0580.

Macromolecule Content

Total Structure Weight: 37.49 kDa
Atom Count: 2,727
Modelled Residue Count: 345
Deposited Residue Count: 345
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ISOPROPYLMALATE DEHYDROGENASE	A	345	Thermus thermophilus	Mutation(s): 0 EC: 1.1.1.85
UniProt
Find proteins for Q5SIY4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIY4 Go to UniProtKB: Q5SIY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SIY4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
NAD	Binding MOAD: 1HEX	Ki: 6.15e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Work: 0.182
R-Value Observed: 0.182
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.1	α = 90
b = 105.1	β = 90
c = 190.4	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1994-12-20

Deposition Author(s):

Hurley, J.H.

Revision History (Full details and data files)

Version 1.0: 1994-12-20
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Other