Crystal structure of human WT NDRG3

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 

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This is version 1.2 of the entry. See complete history


Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein.

Kim, K.R.Kim, K.A.Park, J.S.Jang, J.Y.Choi, Y.Lee, H.H.Lee, D.C.Park, K.C.Yeom, Y.I.Kim, H.J.Han, B.W.

(2020) Biomolecules 10

  • DOI: https://doi.org/10.3390/biom10010090
  • Primary Citation of Related Structures:  
    6L4B, 6L4G, 6L4H

  • PubMed Abstract: 

    The N-Myc downstream-regulated gene (NDRG) family belongs to the α/β-hydrolase fold and is known to exert various physiologic functions in cell proliferation, differentiation, and hypoxia-induced cancer metabolism. In particular, NDRG3 is closely related to proliferation and migration of prostate cancer cells, and recent studies reported its implication in lactate-triggered hypoxia responses or tumorigenesis. However, the underlying mechanism for the functions of NDRG3 remains unclear. Here, we report the crystal structure of human NDRG3 at 2.2 Å resolution, with six molecules in an asymmetric unit. While NDRG3 adopts the α/β-hydrolase fold, complete substitution of the canonical catalytic triad residues to non-reactive residues and steric hindrance around the pseudo-active site seem to disable the α/β-hydrolase activity. While NDRG3 shares a high similarity to NDRG2 in terms of amino acid sequence and structure, NDRG3 exhibited remarkable structural differences in a flexible loop corresponding to helix α6 of NDRG2 that is responsible for tumor suppression. Thus, this flexible loop region seems to play a distinct role in oncogenic progression induced by NDRG3. Collectively, our studies could provide structural and biophysical insights into the molecular characteristics of NDRG3.

  • Organizational Affiliation

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NDRG3375Homo sapiensMutation(s): 0 
Gene Names: NDRG3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGV2 (Homo sapiens)
Explore Q9UGV2 
Go to UniProtKB:  Q9UGV2
GTEx:  ENSG00000101079 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGV2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.341α = 90
b = 100.15β = 90.01
c = 110.744γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Data collection
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description