2PD6 | pdb_00002pd6

Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8

• PDB DOI: https://doi.org/10.2210/pdb2PD6/pdb

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


• Deposited: 2007-03-31 Released: 2007-05-08 
• Deposition Author(s): Turnbull, A.P., Salah, E., Gileadi, O., Savitsky, P., Guo, K., Bunkoczi, G., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Models: experimental

Literature

Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8

Turnbull, A.P., Salah, E., Gileadi, O., Savitsky, P., Guo, K., Bunkoczi, G., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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: 112.52 kDa 
• Atom Count: 7,000 
• Modeled Residue Count: 953 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estradiol 17-beta-dehydrogenase 8	A, B, C, D	264	Homo sapiens	Mutation(s): 0  Gene Names: HSD17B8, FABGL, HKE6, RING2 EC: 1.1.1.62 (PDB Primary Data), 1.1.1.239 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92506 (Homo sapiens) Explore Q92506  Go to UniProtKB:  Q92506
PHAROS:  Q92506 GTEx:  ENSG00000204228

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: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.839	α = 90
b = 62.429	β = 99.22
c = 102.439	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Turnbull, A.P., Salah, E., Gileadi, O., Savitsky, P., Guo, K., Bunkoczi, G., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-05-08
  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: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description