2I9P | pdb_00002i9p

Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+

• PDB DOI: https://doi.org/10.2210/pdb2I9P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-09-06 Released: 2006-09-26 
• Deposition Author(s): Kavanagh, K.L., Papagrigoriou, E., Salah, E., Lukacik, P., Smee, C., Burgess, N., von Delft, F., Weigelt, J., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+

Kavanagh, K.L., Papagrigoriou, E., Salah, E., Lukacik, P., Smee, C., Burgess, N., von Delft, F., Weigelt, J., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 138.12 kDa 
• Atom Count: 8,559 
• Modeled Residue Count: 1,175 
• Deposited Residue Count: 1,276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyisobutyrate dehydrogenase	A, B, C, D	319	Homo sapiens	Mutation(s): 0  Gene Names: HIBADH EC: 1.1.1.31
UniProt & NIH Common Fund Data Resources
Find proteins for P31937 (Homo sapiens) Explore P31937  Go to UniProtKB:  P31937
PHAROS:  P31937 GTEx:  ENSG00000106049

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.220 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.627	α = 90
b = 167.319	β = 107.8
c = 71.089	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-26 
Deposition Author(s): Kavanagh, K.L., Papagrigoriou, E., Salah, E., Lukacik, P., Smee, C., Burgess, N., von Delft, F., Weigelt, J., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description