1HSR | pdb_00001hsr

BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE

• PDB DOI: https://doi.org/10.2210/pdb1HSR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Agaricales sp. 'Arthromyces ramosus
• Mutation(s): No 


• Deposited: 1997-07-01 Released: 1998-07-01 
• Deposition Author(s): Fukuyama, K., Itakura, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Binding mode of benzhydroxamic acid to Arthromyces ramosus peroxidase shown by X-ray crystallographic analysis of the complex at 1.6 A resolution.

Itakura, H., Oda, Y., Fukuyama, K.

(1997) FEBS Lett 412: 107-110

• PubMed: 9257700 
• DOI: https://doi.org/10.1016/s0014-5793(97)00751-5
• Primary Citation Related Structures: 
  1HSR


• PubMed Abstract: 
  

  The crystal structure of Arthromyces ramosus peroxidase (ARP) in complex with benzhydroxamic acid (BHA) as determined by X-ray analysis at 1.6 A shows unambiguously how BHA binds to ARP. BHA is located in the distal heme pocket. Its functional groups are held by three hydrogen bonds to His56N(epsilon), Arg52N(epsilon), and Pro(154)O, but are too far away to interact with the heme iron. The aromatic ring of BHA is positioned at the entrance of the channel to the heme pocket, approximately parallel to the heme group. Most water molecules at the active site of the native enzyme are replaced by BHA, leaving a ligand, probably a water molecule, at the sixth position of the heme. Results are compared with spectroscopic data.

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Organizational Affiliation: 
• Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.98 kDa 
• Atom Count: 2,789 
• Modeled Residue Count: 336 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXIDASE	A	344	Agaricales sp. 'Arthromyces ramosus	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for P28313 (Arthromyces ramosus) Explore P28313  Go to UniProtKB:  P28313
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BHO	F [auth A]	BENZHYDROXAMIC ACID C7 H7 N O2 VDEUYMSGMPQMIK-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.5	α = 90
b = 74.5	β = 90
c = 118.01	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-07-01 
Deposition Author(s): Fukuyama, K., Itakura, H.

Revision History  

• Version 1.0: 1998-07-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary