9KEA | pdb_00009kea

Crystal structure of LnzB (Streptomyces spp. )

PDB DOI: https://doi.org/10.2210/pdb9KEA/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces parvus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-04 Released: 2025-11-12
Deposition Author(s): Zhang, Z.M., Wang, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.242 (Depositor), 0.245 (DCC)
R-Value Work:
0.206 (Depositor), 0.211 (DCC)
R-Value Observed:
0.208 (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

Crystal structure of LnzB (Streptomyces spp. )

Zhang, Z.M., Wang, L.

To be published.

Macromolecule Content

Total Structure Weight: 102.91 kDa
Atom Count: 7,055
Modeled Residue Count: 818
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-binding negative transcriptional regulator	A, B, C, D	223	Streptomyces parvus	Mutation(s): 0 Gene Names: G3I50_12820
UniProt
Find proteins for A0A7K3RVR3 (Streptomyces parvus) Explore A0A7K3RVR3 Go to UniProtKB: A0A7K3RVR3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7K3RVR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 S [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], N [auth C], S [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D], W [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]