3CRB | pdb_00003crb

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

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
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This is version 2.2 of the entry. See complete history. 


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.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactotransferrin345Bos taurusMutation(s): 0 
EC: 3.4.21
UniProt
Find proteins for P24627 (Bos taurus)
Explore P24627 
Go to UniProtKB:  P24627
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24627
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COU
Query on COU
Download Ideal Coordinates CCD File 
J [auth A]COUMARIN
C9 H6 O2
ZYGHJZDHTFUPRJ-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3
Query on CO3
Download Ideal Coordinates CCD File 
F [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE
Query on FE
Download Ideal Coordinates CCD File 
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 = 63.37α = 90
b = 50.37β = 107.81
c = 65.84γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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