3VDF

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with diaminopimelic acid at 1.46 A Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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Literature

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with diaminopimelic acid at 1.46 A Resolution

Shukla, P.K., Gautam, L., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactotransferrin335Bos 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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-TERMINAL PEPTIDE OF LACTOTRANSFERRIN6Bos taurusMutation(s): 0 
EC: 3.4.21
UniProt
Find proteins for P24627 (Bos taurus)
Explore P24627 
Go to UniProtKB:  P24627
Entity Groups  
UniProt GroupP24627
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
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E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
API
Query on API
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K [auth A]2,6-DIAMINOPIMELIC ACID
C7 H14 N2 O4
GMKMEZVLHJARHF-SYDPRGILSA-N
SO4
Query on SO4
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J [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN
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G [auth A],
H [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3
Query on CO3
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I [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE
Query on FE
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F [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.212α = 90
b = 50.023β = 107
c = 65.206γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations