3TOD
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 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.38 Å
- R-Value Free: 0.236 
- R-Value Work: 0.200 
- R-Value Observed: 0.202 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Lactotransferrin | 335 | Bos taurus | Mutation(s): 0  EC: 3.4.21 | ||
UniProt | |||||
Find proteins for P24627 (Bos taurus) Explore P24627  Go to UniProtKB:  P24627 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P24627 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
peptide, LEACAF from Lactotransferrin | 6 | Bos taurus | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P24627 (Bos taurus) Explore P24627  Go to UniProtKB:  P24627 | |||||
Entity Groups   | |||||
UniProt Group | P24627 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
XXB Query on XXB | O [auth A] | 1-butyl-1H-pyrazole-5-carboxylic acid C8 H12 N2 O2 GPCNIDIHJOJQFF-UHFFFAOYSA-N | |||
SO4 Query on SO4 | J [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | K [auth A], L [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ZN Query on ZN | G [auth A], H [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CO3 Query on CO3 | I [auth A] | CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L | |||
FE Query on FE | F [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N | |||
EOH Query on 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 
- R-Value Work: 0.200 
- R-Value Observed: 0.202 
- 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 Name | Purpose |
---|---|
HKL-2000 | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
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 (Full details and data files)
- 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