9KB0 | pdb_00009kb0

3-hydroxyisobutyrate dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb9KB0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Micromonospora echinaurantiaca
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-30 Released: 2025-11-05
Deposition Author(s): Fang, P., Liu, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.223 (Depositor), 0.226 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of 3-hydroxyisobutyrate dehydrogenase complexing with NADPH

Fang, P., Liu, Z.

To be published.

Macromolecule Content

Total Structure Weight: 62.26 kDa
Atom Count: 4,175
Modeled Residue Count: 574
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyisobutyrate dehydrogenase	A, B [auth C]	301	Micromonospora echinaurantiaca	Mutation(s): 0 Gene Names: GA0070609_2033
UniProt
Find proteins for A0A1C5HQ65 (Micromonospora echinaurantiaca) Explore A0A1C5HQ65 Go to UniProtKB: A0A1C5HQ65
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1C5HQ65
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain C [auth A] MOL2 format, chain D [auth C] MOL2 format, chain C [auth A] mmCIF format, chain D [auth C] mmCIF format, chain C [auth A]	C [auth A], D [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-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: 2.90 Å
R-Value Free: 0.223 (Depositor), 0.226 (DCC)
R-Value Work: 0.204 (Depositor), 0.205 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.03	α = 90
b = 65.64	β = 100.23
c = 86.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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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.