1YB1 | pdb_00001yb1

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.192 (Depositor), 0.197 (DCC)
R-Value Work:
0.162 (Depositor), 0.173 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AOI Query on AOI Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B]	Androsterone C₁₉ H₃₀ O₂ QGXBDMJGAMFCBF-HLUDHZFRSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.192 (Depositor), 0.197 (DCC)
R-Value Work: 0.162 (Depositor), 0.173 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-12-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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

1YB1 | pdb_00001yb1

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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