8YKR | pdb_00008ykr

Enhancing the Gastric Stability of Ferritin Nanocage via Computational-Assisted Disulfide Bond Engineering

PDB DOI: https://doi.org/10.2210/pdb8YKR/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Penaeus japonicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-03-05 Released: 2025-03-19
Deposition Author(s): Gu, C.K., Wang, S.J., Zhao, G.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Enhancing the Gastric Stability of Ferritin Nanocage via Computational-Assisted Disulfide Bond Engineering

Gu, C.K., Wang, S.J., Zhao, G.H.

To be published.

Macromolecule Content

Total Structure Weight: 117.23 kDa
Atom Count: 8,097
Modeled Residue Count: 1,006
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F	170	Penaeus japonicus	Mutation(s): 8 EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus) Explore T2B7E1 Go to UniProtKB: T2B7E1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	T2B7E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth A] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B] H [auth B] I [auth A] J [auth C] K [auth D] G [auth B], H [auth B], I [auth A], J [auth C], K [auth D], L [auth D], M [auth E], N [auth E], O [auth F], P [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]