9JN6 | pdb_00009jn6

Crystal structure of KtzT-C197A in complex with HEME and product

PDB DOI: https://doi.org/10.2210/pdb9JN6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Kutzneria sp. 744
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-09-22 Released: 2025-01-29
Deposition Author(s): Li, Y.L., Yang, Y.Y., Huang, J.-W., Chen, C.-C., Guo, R.-T.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.222 (Depositor), 0.229 (DCC)
R-Value Work:
0.187 (Depositor), 0.196 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: in silico
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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

Structural Insights into the N-N Bond-Formation Mechanism of the Heme-Dependent Piperazate Synthase KtzT

Yang, Y., Li, Y., Yao, L., Dai, K., Fu, X., Ge, A., Huang, J.W., Guo, R.T., Chen, C.C.

(2025) ACS Catal 15: 1265-1273

DOI: https://doi.org/10.1021/acscatal.4c06124

Macromolecule Content

Total Structure Weight: 95.85 kDa
Atom Count: 7,493
Modelled Residue Count: 852
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-binding protein	A [auth B], B [auth C], C [auth D], D [auth A]	218	Kutzneria sp. 744	Mutation(s): 1 Gene Names: KUTG_08928
UniProt
Find proteins for A8CF72 (Kutzneria sp. (strain 744)) Explore A8CF72 Go to UniProtKB: A8CF72
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8CF72
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain J [auth A] SDF format, chain E [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain J [auth A] MOL2 format, chain E [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain J [auth A] mmCIF format, chain E [auth B]	E [auth B], G [auth C], H [auth D], J [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth B] Focus chain G [auth C] Focus chain H [auth D] Focus chain J [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth C] Focus chain H [auth D] Focus chain J [auth A]
A1ECN (Subject of Investigation/LOI) Query on A1ECN Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth D] SDF format, chain K [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth D] MOL2 format, chain K [auth A] mmCIF format, chain F [auth B] mmCIF format, chain I [auth D] mmCIF format, chain K [auth A]	F [auth B], I [auth D], K [auth A]	(3~{S})-1,2-diazinane-3-carboxylic acid C₅ H₁₀ N₂ O₂ BZIBRGSBQKLEDC-BYPYZUCNSA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Focus chain K [auth A] Interactions & Density Focus chain F [auth B] Focus chain I [auth D] Focus chain K [auth A]