4NED | pdb_00004ned

Crystal STRUCTURE OF C-LOBE OF BOVINE LACTOFERRIN COMPLEXED WITH FENOPROFEN AT 2.1 ANGSTROM RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb4NED/pdb

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


• Deposited: 2013-10-29 Released: 2013-12-11 
• Deposition Author(s): Gautam, L., Dube, D., Sinha, M., 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: 
  0.252 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal STRUCTURE OF C-LOBE OF BOVINE LACTOFERRIN COMPLEXED WITH FENOPROFEN AT 2.1 ANGSTROM RESOLUTION

Gautam, L., Dube, D., 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: 39.11 kDa 
• Atom Count: 2,894 
• Modeled Residue Count: 341 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactotransferrin	A	345	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: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PFN	I [auth A]	FENOPROFEN C15 H14 O3 RDJGLLICXDHJDY-LLVKDONJSA-N
NAG	G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3	E [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.252 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.47	α = 90
b = 50.07	β = 107.32
c = 65.49	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Gautam, L., Dube, D., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2013-12-11
  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: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary