4C83
Crystal Structure of the IgG2a LPT3 in complex with an 8-sugar inner core analogue of Neisseria meningitidis
- PDB DOI: https://doi.org/10.2210/pdb4C83/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No
- Deposited: 2013-09-29 Released: 2014-02-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.69 Å
- R-Value Free: 0.293
- R-Value Work: 0.225
- R-Value Observed: 0.228
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 |
| LPT3 HEAVY CHAIN | 220 | Mus musculus | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| LPT3 LIGHT CHAIN | 214 | Mus musculus | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]L-glycero-alpha-D-manno-heptopyranose-(1-5)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid | E, F | 5 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G33414YG GlyCosmos: G33414YG | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | G [auth A], H [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.69 Å
- R-Value Free: 0.293
- R-Value Work: 0.225
- R-Value Observed: 0.228
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 62.628 | α = 87.51 |
| b = 64.192 | β = 89.82 |
| c = 64.403 | γ = 73.41 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2014-02-12 Deposition Author(s): Parker, M.J., Gomery, K., Richard, G., Mackenzie, C.R., Cox, A.D., Richards, J.C., Evans, S.V.
Revision History (Full details and data files)
- Version 1.0: 2014-02-12
Type: Initial release - Version 1.1: 2014-04-16
Changes: Database references - Version 1.2: 2015-09-23
Changes: Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
