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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of 3-hydroxyisobutyrate dehydrogenase complexing with NADPH

Fang, P., Liu, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	C [auth A], D [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.223 (Depositor), 0.225 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Fang, P., Liu, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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