3CRB | pdb_00003crb

Crystal structure of the complex of C-lobe of lactoferrin with 2-chromenone at 2.6 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CRB/pdb

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


• Deposited: 2008-04-05 Released: 2008-04-29 
• Deposition Author(s): Vikram, G., Mir, R., Sinha, M., Singh, N., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of C-lobe of lactoferrin with 2-chromenone at 2.6 A resolution

Vikram, G., Mir, R., Sinha, M., Singh, N., 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: 39.42 kDa 
• Atom Count: 2,852 
• 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: 3

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COU	J [auth A]	COUMARIN C9 H6 O2 ZYGHJZDHTFUPRJ-UHFFFAOYSA-N
SO4	I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3	F [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.37	α = 90
b = 50.37	β = 107.81
c = 65.84	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Vikram, G., Mir, R., Sinha, M., Singh, N., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2008-04-29
  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: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary