6ZDI | pdb_00006zdi

17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 2-fluoro-5-nitrophenol

• PDB DOI: https://doi.org/10.2210/pdb6ZDI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2020-06-14 Released: 2021-01-13 
• Deposition Author(s): Badran, M.J., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 2-fluoro-5-nitrophenol

Badran, M.J., Heine, A., 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: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 29.17 kDa 
• Atom Count: 1,932 
• Modeled Residue Count: 252 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
17-beta-hydroxysteroid dehydrogenase 14	A	270	Homo sapiens	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
QFT (Subject of Investigation/LOI)	D [auth A]	2-fluoranyl-5-nitro-phenol C6 H4 F N O3 WFRLFZAMCVAQLN-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.254	α = 90
b = 91.254	β = 90
c = 133.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Badran, M.J., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary