8KB3 | pdb_00008kb3

Superoxide dismutase

PDB DOI: https://doi.org/10.2210/pdb8KB3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-03 Released: 2024-08-07
Deposition Author(s): Zhai, L., Li, B.Q., Jia, H.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

YdiU regulates Salmonella Oxidative Stress by UMPylation of SodA

Zhai, L., Li, B.Q., Jia, H.H.

To be published.

Macromolecule Content

Total Structure Weight: 47.42 kDa
Atom Count: 3,742
Modeled Residue Count: 412
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn]	A, B	206	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: sodA, STM4055 EC: 1.15.1.1
UniProt
Find proteins for P43019 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P43019 Go to UniProtKB: P43019
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43019
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain L [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain D [auth A]	D [auth A] I [auth A] J [auth A] K [auth B] P [auth B] D [auth A], I [auth A], J [auth A], K [auth B], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A], M [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]