5Y7N | pdb_00005y7n

Crystal structure of AKR1B10 in complex with NADP+ and Androst-4-ene-3-beta-6-alpha-diol

• PDB DOI: https://doi.org/10.2210/pdb5Y7N/pdb

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


• Deposited: 2017-08-17 Released: 2018-08-29 
• Deposition Author(s): Hong, Z., Liping, Z., Cuiyun, L., Wei, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structural determinants for the inhibition of AKR1B10 by steroids

Hong, Z., Cuiyun, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.11 kDa 
• Atom Count: 2,692 
• Modeled Residue Count: 313 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member B10	A	316	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B10, AKR1B11 EC: 1.1.1 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60218 (Homo sapiens) Explore O60218  Go to UniProtKB:  O60218
PHAROS:  O60218 GTEx:  ENSG00000198074

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
8QL	C [auth A]	(3S,6S,8S,9S,10R,13S,14R)-10,13-dimethyl-2,3,6,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,6-diol C19 H30 O2 ILCBKPIQQXGQQW-FHIGQFGOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.864	α = 90
b = 89.864	β = 90
c = 78.309	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling
CrysalisPro	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Hong, Z., Liping, Z., Cuiyun, L., Wei, Z.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary