3GMR
Structure of mouse CD1d in complex with C8Ph, different space group
- PDB DOI: https://doi.org/10.2210/pdb3GMR/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2009-03-14 Released: 2009-11-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.230 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
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 |
T-cell surface glycoprotein CD1d1 | 287 | Mus musculus | Mutation(s): 0  Gene Names: Cd1d1, Cd1.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609 | |||||
IMPC:  MGI:107674 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P11609 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2 microglobulin | 99 | Mus musculus | Mutation(s): 0  Gene Names: B2m | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887 | |||||
IMPC:  MGI:88127 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01887 | ||||
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 | C, D | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | E | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G29616NS GlyCosmos:  G29616NS GlyGen:  G29616NS |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
C8P Query on C8P | F [auth A] | N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide C38 H67 N O9 YEKLGTQAMSELFI-ZORUMLJWSA-N | |||
PLM Query on PLM | G [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
PG4 Query on PG4 | L [auth B] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N | |||
EDO Query on EDO | H [auth A], I [auth A], J [auth A], K [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.230 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 42.27 | α = 90 |
b = 107.23 | β = 90 |
c = 109.42 | γ = 90 |
Software Name | Purpose |
---|---|
MAR345 | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-11-10  Deposition Author(s): Schiefner, A., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2009-11-10
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary