2R9J

Ligand recognition in C-lobe: The crystal structure of the complex of lactoferrin C-lobe with nicotinamide at 2.5 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2R9J/pdb

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


• Deposited: 2007-09-13 Released: 2007-10-09 
• Deposition Author(s): Mir, R., Vikram, G., Singh, N., Kumar, S., Sinha, M., Sharma, S., Kaur, P., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.249 
• R-Value Work: 0.225 

Literature

Ligand recognition in C-lobe: The crystal structure of the complex of lactoferrin C-lobe with nicotinamide at 2.5 A resolution

Mir, R., Vikram, G., Singh, N., Kumar, S., Sinha, M., Sharma, S., Kaur, P., 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: 39.19 kDa 
• Atom Count: 2,867 
• Modelled 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

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, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NCA	J [auth A]	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N
SO4	I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3	H [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.249 
• R-Value Work: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.33	α = 90
b = 50.34	β = 107.65
c = 65.91	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Mir, R., Vikram, G., Singh, N., Kumar, S., Sinha, M., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary