8ZXU | pdb_00008zxu

Crystal structure of N terminal deletion mutant of Staphylococcal atypical two-cysteine thiol peroxidase complexed with substrate analog

PDB DOI: https://doi.org/10.2210/pdb8ZXU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-15 Released: 2025-06-18
Deposition Author(s): Shukla, M., Maji, S., Yadav, V.K., Bhattacharyya, S.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.195 (Depositor), 0.183 (DCC)
R-Value Work:
0.163 (Depositor), 0.153 (DCC)
R-Value Observed:
0.164 (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 N terminal deletion mutant of Staphylococcal atypical two-cysteine thiol peroxidase complexed with substrate analog

Shukla, M., Maji, S., Yadav, V.K., Bhattacharyya, S.

To be published.

Macromolecule Content

Total Structure Weight: 67.95 kDa
Atom Count: 5,479
Modeled Residue Count: 596
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol peroxidase	A, B, C, D	149	Staphylococcus aureus	Mutation(s): 0 Gene Names: tpx, SACOL1762 EC: 1.11.1.24
UniProt
Find proteins for Q5HF61 (Staphylococcus aureus (strain COL)) Explore Q5HF61 Go to UniProtKB: Q5HF61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5HF61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain T [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], T [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth D]
DTO Query on DTO Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL C₄ H₁₀ O₃ S₂ MFLGZMZEMVZQCC-QWWZWVQMSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
DTU Query on DTU Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-ZXZARUISSA-N		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
A1L2G (Subject of Investigation/LOI) Query on A1L2G Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth C] SDF format, chain S [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] mmCIF format, chain J [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D]	J [auth A], R [auth C], S [auth D]	O-tert-Butylhydroxylamine C₄ H₁₁ N O KKVUFSINQFSJNK-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth C] Focus chain S [auth D] Interactions & Density Focus chain J [auth A] Focus chain R [auth C] Focus chain S [auth D]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
PEO Query on PEO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	I [auth A], P [auth B], Q [auth B]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B]