10NH | pdb_000010nh

Crystal Structure of Apurinic endonuclease (APN1) from Babesia bovis

PDB DOI: https://doi.org/10.2210/pdb10NH/pdb

Classification: HYDROLASE
Organism(s): Babesia bovis T2Bo
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-01-28 Released: 2026-02-11
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.264 (Depositor), 0.266 (DCC)
R-Value Work:
0.205 (Depositor), 0.209 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Apurinic endonuclease (APN1) from Babesia bovis

Lovell, S., Cooper, A., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 219.42 kDa
Atom Count: 14,947
Modeled Residue Count: 1,874
Deposited Residue Count: 1,938
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apurinic endonuclease (APN1)	A, B, C, D, E A, B, C, D, E, F	323	Babesia bovis T2Bo	Mutation(s): 0 Gene Names: BBOV_III005900
UniProt
Find proteins for S6B9Y3 (Babesia bovis) Explore S6B9Y3 Go to UniProtKB: S6B9Y3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S6B9Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain DA [auth F] MOL2 format, chain DA [auth F] mmCIF format, chain DA [auth F]	DA [auth F]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Interactions & Density Focus chain DA [auth F]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain Z [auth E] SDF format, chain V [auth D] MOL2 format, chain EA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] mmCIF format, chain EA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D]	EA [auth F] J [auth A] N [auth B] R [auth C] V [auth D] EA [auth F], J [auth A], N [auth B], R [auth C], V [auth D], Z [auth E]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain EA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E]	AA [auth F] BA [auth F] CA [auth F] G [auth A] H [auth A] AA [auth F], BA [auth F], CA [auth F], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], S [auth D], T [auth D], U [auth D], W [auth E], X [auth E], Y [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.264 (Depositor), 0.266 (DCC)
R-Value Work: 0.205 (Depositor), 0.209 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.625	α = 91.66
b = 93.089	β = 91.18
c = 102.879	γ = 91.09

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394