9K5P | pdb_00009k5p

Crystal structure of designed zinc-induced homotrimer C3-Zn2-HEHE-19

PDB DOI: https://doi.org/10.2210/pdb9K5P/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-21 Released: 2025-10-22
Deposition Author(s): Qu, Y.N., Cao, L.X.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.278 (Depositor), 0.277 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

De novo design of metal ion regulated protein assemblies

Qu, Y.N., Cao, L.X.

To be published.

Macromolecule Content

Total Structure Weight: 38.49 kDa
Atom Count: 2,220
Modeled Residue Count: 264
Deposited Residue Count: 336
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C3-Zn2-HEHE-19	A, B, C	112	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], L [auth B], M [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C]