Macromolecule Content

Total Structure Weight: 213.93 kDa
Atom Count: 13631
Residue Count: 1640
Unique protein chains: 1

3U8U

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

DOI: 10.2210/pdb3U8U/pdb

Classification: HYDROLASE, LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-17 Released: 2011-10-26
Deposition Author(s): Agarwal, R., Naidu, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.243
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

Agarwal, R., Naidu, M.D.

To be published.

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) lyase	A, B, C, D, E, F	318	Homo sapiens	Mutation(s): 0 Gene Names: APEX1, APE, APE1, APEX, APX, HAP1, REF1 EC: 3.1 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for P27695 (Homo sapiens) Explore P27695 Go to UniProtKB: P27695
NIH Common Fund Data Resources
PHAROS P27695 GTEx ENSG00000100823
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [A] SDF format, chain J [B] SDF format, chain L [C] SDF format, chain P [F] MOL2 format, chain H [A] MOL2 format, chain J [B] MOL2 format, chain L [C] MOL2 format, chain P [F]	A, B, C, F	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain I [B] SDF format, chain K [C] SDF format, chain M [D] SDF format, chain N [E] SDF format, chain O [F] MOL2 format, chain G [A] MOL2 format, chain I [B] MOL2 format, chain K [C] MOL2 format, chain M [D] MOL2 format, chain N [E] MOL2 format, chain O [F]	A, B, C, D, E, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.243
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.84	α = 90
b = 97.284	β = 90.91
c = 132.15	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Deposited Date: 2011-10-17
Released Date: 2011-10-26

Deposition Author(s):

Revision History

Version 1.0: 2011-10-26
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.