2DS9
Structure of the complex of C-terminal lobe of bovine lactoferrin with mannose at 2.8 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2DS9/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): No
- Deposited: 2006-06-22 Released: 2006-07-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.228
- R-Value Work: 0.196
- R-Value Observed: 0.198
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 |
| alpha-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: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-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 | 6 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G62783KT GlyCosmos: G62783KT GlyGen: G62783KT | |||||
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| MAN Query on MAN | E [auth A] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-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 |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.228
- R-Value Work: 0.196
- R-Value Observed: 0.198
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.818 | α = 90 |
| b = 50.387 | β = 108.08 |
| c = 65.982 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MAR345 | data collection |
| SCALEPACK | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2006-07-04 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: 2006-07-04
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, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
