3T8X
Crystal structure of human CD1b in complex with synthetic antigenic diacylsulfoglycolipid SGL12 and endogenous spacer
- PDB DOI: https://doi.org/10.2210/pdb3T8X/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Mus musculus
- Mutation(s): No 
- Deposited: 2011-08-02 Released: 2011-10-26 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.211 
- R-Value Work: 0.165 
- R-Value Observed: 0.167 
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 CD1b | 301 | Homo sapiens | Mutation(s): 0  Gene Names: CD1B | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P29016 (Homo sapiens) Explore P29016  Go to UniProtKB:  P29016 | |||||
PHAROS:  P29016 GTEx:  ENSG00000158485  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P29016 | ||||
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 | Homo sapiens | Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769 | |||||
PHAROS:  P61769 GTEx:  ENSG00000166710  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, G | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | F | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G00395TQ GlyCosmos:  G00395TQ GlyGen:  G00395TQ |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
T8X Query on T8X | K [auth A], Q [auth C] | 2-O-sulfo-alpha-D-glucopyranosyl
2-O-hexadecanoyl-3-O-[(2E,4S,6S,8S)-2,4,6,8-tetramethyltetracos-2-enoyl]-alpha-D-glucopyranoside C56 H104 O16 S NEVRXHPVRYSQOZ-ZZLYBKFXSA-N | |||
ULI Query on ULI | L [auth A], R [auth C] | tetracontane C40 H82 KUPLEGDPSCCPJI-UHFFFAOYSA-N | |||
SO4 Query on SO4 | I [auth A], O [auth C], P [auth C], S [auth D], T [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | M [auth B], N [auth B], U [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ACT Query on ACT | J [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.211 
- R-Value Work: 0.165 
- R-Value Observed: 0.167 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 203.25 | α = 90 |
b = 67.58 | β = 112.26 |
c = 88.19 | γ = 90 |
Software Name | Purpose |
---|---|
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2011-10-26  Deposition Author(s): Garcia-Alles, L.F., Maveyraud, L., Mourey, L., Julien, S.
Revision History (Full details and data files)
- Version 1.0: 2011-10-26
Type: Initial release - 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: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary