3TOD | pdb_00003tod

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with 1-Butyl-1H-Pyrazole-5-carboxylic acid at 1.38 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb3TOD/pdb

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


• Deposited: 2011-09-05 Released: 2011-09-21 
• Deposition Author(s): Shukla, P.K., Gautam, L., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.236 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with 1-Butyl-1H-Pyrazole-5-carboxylic acid at 1.38 A Resolution

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.34 kDa 
• Atom Count: 3,280 
• Modeled Residue Count: 341 
• Deposited Residue Count: 341 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactotransferrin	A	335	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide, LEACAF from Lactotransferrin	B	6	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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XXB	O [auth A]	1-butyl-1H-pyrazole-5-carboxylic acid C8 H12 N2 O2 GPCNIDIHJOJQFF-UHFFFAOYSA-N
SO4	J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3	I [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	F [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
EOH	M [auth A], N [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.236 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.415	α = 90
b = 49.977	β = 107.14
c = 65.289	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Shukla, P.K., Gautam, L., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• 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