2DXY
Structure of the complex of C-terminal lobe of bovine lactoferrin with trehalose at 2.0 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2DXY/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): No 
- Deposited: 2006-09-03 Released: 2006-09-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.03 Å
- R-Value Free: 0.211 
- R-Value Work: 0.169 
- R-Value Observed: 0.172 
wwPDB Validation   3D Report Full Report
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 | 345 | 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 | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G57221JN GlyCosmos:  G57221JN GlyGen:  G57221JN |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | J [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ZN Query on ZN | F [auth A], G [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 | H [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900006 Query on PRD_900006 | D | trehalose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.03 Å
- R-Value Free: 0.211 
- R-Value Work: 0.169 
- R-Value Observed: 0.172 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 63.374 | α = 90 |
b = 50.413 | β = 107.81 |
c = 65.909 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MAR345 | data collection |
AUTOMAR | data reduction |
AMoRE | phasing |
Entry History 
Deposition Data
- Released Date: 2006-09-19  Deposition Author(s): Mir, R., Singh, N., Sinha, M., Sharma, S., Bhushan, A., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2006-09-19
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-11
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary