4F7C
Crystal structure of bovine CD1d with bound C12-di-sulfatide
- PDB DOI: https://doi.org/10.2210/pdb4F7C/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Bos taurus
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2012-05-15 Released: 2012-11-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.86 Å
- R-Value Free: 0.291 
- R-Value Work: 0.222 
- R-Value Observed: 0.225 
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 |
CD1D antigen, d polypeptide | 283 | Bos taurus | Mutation(s): 0  Gene Names: CD1D | ||
UniProt | |||||
Find proteins for A1L565 (Bos taurus) Explore A1L565  Go to UniProtKB:  A1L565 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1L565 | ||||
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 |
Beta-2-microglobulin | 98 | Bos taurus | Mutation(s): 0  Gene Names: B2M | ||
UniProt | |||||
Find proteins for P01888 (Bos taurus) Explore P01888  Go to UniProtKB:  P01888 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01888 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | F, G | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | H | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G31886NL GlyCosmos:  G31886NL GlyGen:  G31886NL |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
0SG Query on 0SG | I [auth A], J [auth C] | N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}dodecanamide C36 H69 N O14 S2 JBJSVLZKWGLXMO-AZNTWQPMSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.86 Å
- R-Value Free: 0.291 
- R-Value Work: 0.222 
- R-Value Observed: 0.225 
- Space Group: P 42
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 168.553 | α = 90 |
b = 168.553 | β = 90 |
c = 41.525 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2012-11-14  Deposition Author(s): Wang, J., Zajonc, D.M.
Revision History (Full details and data files)
- Version 1.0: 2012-11-14
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary