8U3P

1.79 Angstrom resolution crystal structure of KatG from Mycobacterium tuberculosis with an MYW cofactor after heat incubation for 60 minutes

PDB DOI: https://doi.org/10.2210/pdb8U3P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-08 Released: 2024-09-11
Deposition Author(s): Liu, A., Li, J., Ran, D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.220
R-Value Work: 0.179
R-Value Observed: 0.179

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

1.79 Angstrom resolution crystal structure of KatG from Mycobacterium tuberculosis with an MYW cofactor after heat incubation for 60 minutes

Liu, A., Li, J., Ran, D.

To be published.

Macromolecule Content

Total Structure Weight: 327.37 kDa
Atom Count: 25,857
Modelled Residue Count: 2,868
Deposited Residue Count: 2,964
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B, C, D	741	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: katG EC: 1.11.1.21
UniProt
Find proteins for A0A0D5ZBI4 (Mycobacterium tuberculosis) Explore A0A0D5ZBI4 Go to UniProtKB: A0A0D5ZBI4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0D5ZBI4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D]	F [auth A], M [auth B], V [auth C], Z [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain V [auth C] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	AA [auth D], G [auth A], N [auth B], O [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D]	E [auth A], L [auth B], U [auth C], Y [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain U [auth C] Focus chain Y [auth D]