3GUG | pdb_00003gug

Crystal structure of AKR1C1 L308V mutant in complex with NADP and 3,5-dichlorosalicylic acid

• PDB DOI: https://doi.org/10.2210/pdb3GUG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-03-30 Released: 2010-02-09 
• Deposition Author(s): Dhagat, U., El-Kabbani, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AKR1C1 L308V mutant in complex with NADP and 3,5-dichlorosalicylic acid

Dhagat, U., Hara, A., El-Kabbani, O.

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)

Macromolecule Content 

• Total Structure Weight: 37.84 kDa 
• Atom Count: 2,938 
• Modeled Residue Count: 318 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C1	A	323	Homo sapiens	Mutation(s): 1  Gene Names: AKR1C1, DDH, DDH1 EC: 1.1.1 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.209 (UniProt), 1.3.1.20 (UniProt), 1.1.1.51 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (UniProt), 1.1.1.210 (UniProt), 1.1.1.149 (UniProt), 1.1.1.112 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q04828 (Homo sapiens) Explore Q04828  Go to UniProtKB:  Q04828
PHAROS:  Q04828 GTEx:  ENSG00000187134

Small Molecules

Ligands 3 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
C2U	C [auth A]	3,5-dichloro-2-hydroxybenzoic acid C7 H4 Cl2 O3 CNJGWCQEGROXEE-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C2U	BindingDB:  3GUG	Ki: min: 5.9, max: 2800 (nM) from 8 assay(s)
		IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.412	α = 90
b = 83.885	β = 90.98
c = 48.914	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Dhagat, U., El-Kabbani, O.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description