11KK | pdb_000011kk

Crystal structure of HerA Like Helicae YjgR with NTPase fold from Escherchia coli

PDB DOI: https://doi.org/10.2210/pdb11KK/pdb

Classification: GENE REGULATION
Organism(s): Escherichia coli str. K-12 substr. MG1655
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-03-01 Released: 2026-05-06
Deposition Author(s): Kim, Y., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of HerA Like Helicae YjgR with NTPase fold from Escherchia coli

Kim, Y., Maltseva, N., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 334.74 kDa
Atom Count: 22,184
Modeled Residue Count: 2,873
Deposited Residue Count: 3,018
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HerA like helicase YjgR	A, B, C, D, E A, B, C, D, E, F	503	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Gene Names: yjgR, b4263, JW4220
UniProt
Find proteins for P39342 (Escherichia coli (strain K12)) Explore P39342 Go to UniProtKB: P39342
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39342
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F]	G [auth A] H [auth B] J [auth C] K [auth D] M [auth E] G [auth A], H [auth B], J [auth C], K [auth D], M [auth E], N [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D] mmCIF format, chain I [auth B] mmCIF format, chain L [auth D]	I [auth B], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth D]