7EVQ | pdb_00007evq

Crystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using pepsin at 2.6 A resolution

• PDB DOI: https://doi.org/10.2210/pdb7EVQ/pdb

• Classification: IRON-BINDING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2021-05-21 Released: 2021-06-09 
• Deposition Author(s): Viswanathan, V., Singh, J., Sharma, P., Sharma, S., Singh, T.P.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using pepsin at 2.6 A resolution

Viswanathan, V., Singh, J., Sharma, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 79.11 kDa 
• Atom Count: 5,593 
• Modeled Residue Count: 696 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactotransferrin	A, B	348	Bos taurus	Mutation(s): 0  EC: 3.4.21
UniProt
Find proteins for P24627 (Bos taurus) Explore P24627  Go to UniProtKB:  P24627
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	I [auth A], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)	H [auth A], M [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE (Subject of Investigation/LOI)	G [auth A], L [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.246	α = 90
b = 81.69	β = 129.907
c = 110.227	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Viswanathan, V., Singh, J., Sharma, P., Sharma, S., Singh, T.P.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	PDF/2018/000008

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary