4Y55 | pdb_00004y55

Crystal structure of Buffalo lactoperoxidase with Rhodanide at 2.09 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4Y55/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bubalus bubalis
• Mutation(s): No 


• Deposited: 2015-02-11 Released: 2015-03-25 
• Deposition Author(s): Gupta, A., Tyagi, T.K., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.298 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Buffalo lactoperoxidase with Rhodanide at 2.09 Angstrom resolution

Gupta, A., Tyagi, T.K., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.74 kDa 
• Atom Count: 5,156 
• Modeled Residue Count: 595 
• Deposited Residue Count: 595 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A	595	Bubalus bubalis	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for A5JUY8 (Bubalus bubalis) Explore A5JUY8  Go to UniProtKB:  A5JUY8
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	P [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
IOD	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], U [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
NO3	L [auth A], M [auth A], N [auth A], O [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
SCN	Q [auth A], R [auth A], S [auth A], T [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.298 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.012	α = 90
b = 80.047	β = 102.64
c = 76.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
PDB_EXTRACT	data extraction
AUTOMAR	data reduction
AUTOMAR	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Gupta, A., Tyagi, T.K., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary