8ZXR | pdb_00008zxr

Experimental Data Snapshot

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

(2025) Proteins 93: 949-956

PubMed Abstract:
Domain related to iron (DRI) contains approximately 90 residues and is involved in iron and heme metabolism. Recent discoveries have annotated Dri1, a DRI-only protein from the cyanobacterium Synechocystis, as a regulator of succinate dehydrogenase in a b-type heme-dependent manner or as a c-type heme oxygenase. Here, we report high-resolution structures of Dri1 in complex with b-type and c-type hemes, respectively. Bis-His-ligated heme is located in the middle of the dimeric Dri1 complex with heme b, as well as in the complex of monomeric Dri1 with c-type heme, but distinct heme binding modes are revealed. Structural analyses suggest that Dri1 may participate in the succinate dehydrogenase activity and/or the metabolism of cytochromes.

Organizational Affiliation

Macromolecule Content

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ssr1698 protein	A	105	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: ssr1698
UniProt
Find proteins for P73129 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73129 Go to UniProtKB: P73129
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P73129
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	B	11	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P00004 (Equus caballus) Explore P00004 Go to UniProtKB: P00004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00004
Sequence Annotations Expand
Reference Sequence

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]