1TH3 | pdb_00001th3

Crystal structure of NADPH depleted bovine live catalase complexed with cyanide

• PDB DOI: https://doi.org/10.2210/pdb1TH3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2004-06-01 Released: 2005-07-05 
• Deposition Author(s): Sugadev, R., Balasundaresan, D., Ponnuswamy, M.N., Kumaran, D., Swaminathan, S., Sekar, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of bovine liver catalase

Sugadev, R., Balasundaresan, D., Ponnuswamy, M.N., Kumaran, D., Swaminathan, S., Sekar, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 233.18 kDa 
• Atom Count: 16,932 
• Modeled Residue Count: 1,996 
• Deposited Residue Count: 2,024 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A, B, C, D	506	Bos taurus	Mutation(s): 0  EC: 1.11.1.6
UniProt
Find proteins for P00432 (Bos taurus) Explore P00432  Go to UniProtKB:  P00432

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A], G [auth B], H [auth C], J [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CYN	E [auth A], I [auth D]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.06	α = 90
b = 140.11	β = 90
c = 226.51	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-05 
Deposition Author(s): Sugadev, R., Balasundaresan, D., Ponnuswamy, M.N., Kumaran, D., Swaminathan, S., Sekar, K.

Revision History  

• Version 1.0: 2005-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description