6M7E | pdb_00006m7e

Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.

• PDB DOI: https://doi.org/10.2210/pdb6M7E/pdb
• Entry: 6M7E supersedes: 4GN6

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


• Deposited: 2020-03-18 Released: 2020-04-15 
• Deposition Author(s): Maurya, A., Viswanathan, V., Pandey, N., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.269 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.187 (DCC) 

Starting Model: experimental

Literature

Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.

Maurya, A., Viswanathan, V., Pandey, N., Singh, A.K., Sinha, M., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.99 kDa 
• Atom Count: 5,116 
• 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	Bos taurus	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for P80025 (Bos taurus) Explore P80025  Go to UniProtKB:  P80025
Glycosylation
Glycosylation Sites: 4

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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD (Subject of Investigation/LOI)	AA [auth A], BA [auth A], CA [auth A], DA [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], X [auth A], Y [auth A], Z [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL (Subject of Investigation/LOI)	R [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OSM (Subject of Investigation/LOI)	U [auth A]	1-(OXIDOSULFANYL)METHANAMINE C H5 N O S KONFWJXIYYGXOO-UHFFFAOYSA-N
SCN (Subject of Investigation/LOI)	Q [auth A], S [auth A], T [auth A], V [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA (Subject of Investigation/LOI)	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.269 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.187 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.81	α = 90
b = 80.673	β = 103.07
c = 74.442	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Maurya, A., Viswanathan, V., Pandey, N., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.
• This entry supersedes: 4GN6

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2022-05-04
  Changes: Database references, Structure summary
• Version 2.2: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.3: 2024-11-13
  Changes: Structure summary