8HNQ | pdb_00008hnq

The structure of a alcohol dehydrogenase AKR13B2 with NADP

• PDB DOI: https://doi.org/10.2210/pdb8HNQ/pdb

• Classification: TOXIN
• Organism(s): Devosia sp. D6-9
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-08 Released: 2023-12-20 
• Deposition Author(s): Chen, M., Yang, H., Lu, F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

The structure of AKR13B2

Chen, M., Yang, H., Lu, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.72 kDa 
• Atom Count: 2,722 
• Modeled Residue Count: 286 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-dependent aldo/keto reductase AKR13B2	A	286	Devosia sp. D6-9	Mutation(s): 0  Gene Names: AKR13B2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
O4B (Subject of Investigation/LOI)	D [auth A], E [auth A]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C12 H24 O6 XEZNGIUYQVAUSS-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.114	α = 90
b = 67.582	β = 90
c = 87.487	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Chen, M., Yang, H., Lu, F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release