Crystal structure of human heme oxygenase 1 (HO-1) in complex with its substrate heme, crystal form B

Experimental Data Snapshot

  • Resolution: 2.58 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Comparison of the heme-free and -bound crystal structures of human heme oxygenase-1

Lad, L.Schuller, D.J.Shimizu, H.Friedman, J.Li, H.Ortiz de Montellano, P.R.Poulos, T.L.

(2003) J Biol Chem 278: 7834-7843

  • DOI: https://doi.org/10.1074/jbc.M211450200
  • Primary Citation of Related Structures:  
    1N3U, 1N45, 1NI6

  • PubMed Abstract: 

    Heme oxygenase (HO) catalyzes the degradation of heme to biliverdin. The crystal structure of human HO-1 in complex with heme reveals a novel helical structure with conserved glycines in the distal helix, providing flexibility to accommodate substrate binding and product release (Schuller, D. J., Wilks, A., Ortiz de Montellano, P. R., and Poulos, T. L. (1999) Nat. Struct. Biol. 6, 860-867). To structurally understand the HO catalytic pathway in more detail, we have determined the crystal structure of human apo-HO-1 at 2.1 A and a higher resolution structure of human HO-1 in complex with heme at 1.5 A. Although the 1.5-A heme.HO-1 model confirms our initial analysis based on the 2.08-A model, the higher resolution structure has revealed important new details such as a solvent H-bonded network in the active site that may be important for catalysis. Because of the absence of the heme, the distal and proximal helices that bracket the heme plane in the holo structure move farther apart in the apo structure, thus increasing the size of the active-site pocket. Nevertheless, the relative positioning and conformation of critical catalytic residues remain unchanged in the apo structure compared with the holo structure, but an important solvent H-bonded network is missing in the apoenzyme. It thus appears that the binding of heme and a tightening of the structure around the heme stabilize the solvent H-bonded network required for proper catalysis.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Program in Macromolecular Structure, University of California, Irvine 92697, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
heme oxygenase 1
A, B
233Homo sapiensMutation(s): 0 
Gene Names: HMOX1HO1
UniProt & NIH Common Fund Data Resources
Find proteins for P09601 (Homo sapiens)
Explore P09601 
Go to UniProtKB:  P09601
GTEx:  ENSG00000100292 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09601
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.58 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.395α = 90
b = 55.92β = 101.2
c = 79.379γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description