6GTB | pdb_00006gtb

17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with FB211

• PDB DOI: https://doi.org/10.2210/pdb6GTB/pdb

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


• Deposited: 2018-06-18 Released: 2019-09-11 
• Deposition Author(s): Bertoletti, N., Marchais-Oberwinkler, S., Heine, A., Klebe, G.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystallographic Fragment screening and Hit Optimization

Bertoletti, N., Braun, F., Zara, L., Metz, A., Heine, A., Marchais-Oberwinkler, S., Klebe, G.

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)

Biological Assembly Evidence: gel filtration, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 29.98 kDa 
• Atom Count: 2,205 
• Modeled Residue Count: 257 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
17-beta-hydroxysteroid dehydrogenase 14	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 EC: 1.1.1 (PDB Primary Data), 1.1.1.122 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BPX1 (Homo sapiens) Explore Q9BPX1  Go to UniProtKB:  Q9BPX1
PHAROS:  Q9BPX1 GTEx:  ENSG00000087076

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
FBK	E [auth A]	3-[6-(3-hydroxyphenyl)pyridin-2-yl]benzoic acid C18 H13 N O3 RGVPEEGFSSWQPL-UHFFFAOYSA-N
BGC	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
DMS	G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.338	α = 90
b = 91.338	β = 90
c = 133.065	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
Coot	model building
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Bertoletti, N., Marchais-Oberwinkler, S., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	MA-5287/1-1
German Research Foundation	Germany	KL-1204/15-1

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-23
  Changes: Structure summary