7MEV

Human Apex/Ref1 monomer with C138A mutation

• PDB DOI: https://doi.org/10.2210/pdb7MEV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-04-07 Released: 2022-04-13 
• Deposition Author(s): Nam, Y.W., Yang, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

The Development of Novel Apurinic/Aprymidinic Endonuclease/Redox-factor 1 Inhibitors for the Treatment of Human Melanoma

Nam, Y.W., Khanjani, E.B., Fong, S., Chawla, S., Rahighi, S., Ibrahim, N., Parang, K., Zhang, M., Yang, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 31.43 kDa 
• Atom Count: 2,460 
• Modelled Residue Count: 275 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial	A	276	Homo sapiens	Mutation(s): 1  Gene Names: APEX1, APE, APE1, APEX, APX, HAP1, REF1
UniProt & NIH Common Fund Data Resources
Find proteins for P27695 (Homo sapiens) Explore P27695  Go to UniProtKB:  P27695
PHAROS:  P27695 GTEx:  ENSG00000100823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.242	α = 90
b = 74.447	β = 111.61
c = 45.279	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
XPREP	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Nam, Y.W., Yang, S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	K08CA179084

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description