2O23

The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A

• PDB DOI: https://doi.org/10.2210/pdb2O23/pdb

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


• Deposited: 2006-11-29 Released: 2006-12-12 
• Deposition Author(s): Kavanagh, K.L., Shafqat, N., Scholer, K., Debreczeni, J., Zschocke, J., 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: 1.20 Å
• R-Value Free: 0.154 
• R-Value Work: 0.123 
• R-Value Observed: 0.123 

Starting Model: experimental

Literature

The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A

KAVANAGH, K.L., SHAFQAT, N., SCHOLER, K., DEBRECZENI, J., ZSCHOCKE, J., 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,PQS (software)

Macromolecule Content

• Total Structure Weight: 55.99 kDa 
• Atom Count: 4,458 
• Modelled Residue Count: 503 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HADH2 protein	A, B	265	Homo sapiens	Mutation(s): 0  Gene Names: HADH2 EC: 1.1.1.178 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1.239 (UniProt), 1.1.1.159 (UniProt), 1.1.1.35 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99714 (Homo sapiens) Explore Q99714  Go to UniProtKB:  Q99714
PHAROS:  Q99714 GTEx:  ENSG00000072506

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.154 
• R-Value Work: 0.123 
• R-Value Observed: 0.123 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.037	α = 90
b = 117.037	β = 90
c = 69.087	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Kavanagh, K.L., Shafqat, N., Scholer, K., Debreczeni, J., Zschocke, J., von Delft, F., Weigelt, J., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description