28EO | pdb_000028eo

Crystal structure of heme oxygenase from Corynebacterium diphtheriae (HmuO) in complex with hydroperoxo-heme

PDB DOI: https://doi.org/10.2210/pdb28EO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-06-23 Released: 2026-10-28
Deposition Author(s): Unno, M., Ikeda-Saito, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystallographic snapshots of heme oxygenase meso-hydroxylation achieved with X-ray-induced photoreduction and annealing.

Unno, M., Matsui, T., Ikeda-Saito, M.

(2026) Coord Chem Res

DOI: https://doi.org/10.1016/j.cocr.2026.100048

Macromolecule Content

Total Structure Weight: 75.86 kDa
Atom Count: 5,997
Modeled Residue Count: 628
Deposited Residue Count: 645
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heme oxygenase (biliverdin-producing)	A, B, C	215	Corynebacterium diphtheriae	Mutation(s): 0 EC: 1.14.14.18
UniProt
Find proteins for Q54AI1 (Corynebacterium diphtheriae) Explore Q54AI1 Go to UniProtKB: Q54AI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q54AI1
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 D [auth A] SDF format, chain M [auth B] SDF format, chain V [auth C] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C]	D [auth A], M [auth B], V [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain M [auth B] Focus chain V [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth B] Focus chain V [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain S [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain S [auth B]	AA [auth C] F [auth A] G [auth A] H [auth A] O [auth B] AA [auth C], F [auth A], G [auth A], H [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
PEO Query on PEO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B]	E [auth A], N [auth B]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain K [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A]	BA [auth C] CA [auth C] I [auth A] J [auth A] K [auth A] BA [auth C], CA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B]