1YB1

Crystal structure of human 17-beta-hydroxysteroid dehydrogenase type XI

• PDB DOI: https://doi.org/10.2210/pdb1YB1/pdb

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


• Deposited: 2004-12-18 Released: 2004-12-28 
• Deposition Author(s): Lukacik, P., Bunkoczi, G., Kavanagh, K., Ng, S., von Delft, F., Bray, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human 17-beta-hydroxysteroid dehydrogenase type XI.

Lukacik, P., Bunkoczi, G., Kavanagh, K., Ng, S., von Delft, F., Bray, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Oppermann, U.

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)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.48 kDa 
• Atom Count: 4,111 
• Modelled Residue Count: 485 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
17-beta-hydroxysteroid dehydrogenase type XI	A, B	272	Homo sapiens	Mutation(s): 0  Gene Names: DHRS8 EC: 1.1.1.62
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBQ5 (Homo sapiens) Explore Q8NBQ5  Go to UniProtKB:  Q8NBQ5
PHAROS:  Q8NBQ5 GTEx:  ENSG00000198189

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AOI	H [auth A], L [auth B]	Androsterone C19 H30 O2 QGXBDMJGAMFCBF-HLUDHZFRSA-N
SO4	F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.939	α = 90
b = 110.939	β = 90
c = 118.013	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-28 
Deposition Author(s): Lukacik, P., Bunkoczi, G., Kavanagh, K., Ng, S., von Delft, F., Bray, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2013-07-03
  Changes: Non-polymer description
• Version 1.4: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-04-03
  Changes: Refinement description