2ISI | pdb_00002isi

Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand

• PDB DOI: https://doi.org/10.2210/pdb2ISI/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-10-17 Released: 2006-10-31 
• Deposition Author(s): Agarwal, R., Naidu, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Crystal structure of hApe1 in a new crystal form with a bound ligand: implications on catalytic mechanism and its inhibition

Agarwal, R., Naidu, M.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 106.69 kDa 
• Atom Count: 6,610 
• Modeled Residue Count: 825 
• Deposited Residue Count: 951 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) lyase	A, B, C	317	Homo sapiens	Mutation(s): 0  EC: 4.2.99.18 (PDB Primary Data), 3.1.21 (UniProt), 3.1.11.2 (UniProt)
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
PO4	D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	E [auth A], G [auth B], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.220 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.347	α = 90
b = 92.392	β = 121.38
c = 94.006	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): Agarwal, R., Naidu, M.D.

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary