4GPF

Structure of the Fe3+-biliverdin-HmuO, heme oxygenase from Corynebacterium diphtheriae (data set III)

PDB DOI: https://doi.org/10.2210/pdb4GPF/pdb

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

Deposited: 2012-08-20 Released: 2013-08-21
Deposition Author(s): Unno, M., Ikeda-Saito, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.239
R-Value Work: 0.185
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Substrate-Free and the Product-Bound forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae

Unno, M., Ardevol, A., Rovira, C., Ikeda-Saito, M.

To be published.

Macromolecule Content

Total Structure Weight: 75.47 kDa
Atom Count: 5,494
Modelled Residue Count: 624
Deposited Residue Count: 645
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase	A, B, C	215	Corynebacterium diphtheriae	Mutation(s): 0 EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt
Find proteins for Q54AI1 (Corynebacterium diphtheriae) Explore Q54AI1 Go to UniProtKB: Q54AI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q54AI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA Query on BLA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain S [auth C] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B]	D [auth A], N [auth B], S [auth C]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain N [auth B] Focus chain S [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain G [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	F [auth A] G [auth A] H [auth A] I [auth B] J [auth B] F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] 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] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] 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]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]