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
Deposition Author(s): Garcia-Alles, L.F., Maveyraud, L., Mourey, L., Julien, S.

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structural reorganization of the human CD1b Antigen-binding groove for presentation of mycobacterial sulfoglycolipids

Garcia-Alles, L.F., Collmann, A., Versluis, C., Lindner, B., Guiard, J., Maveyraud, L., Huc, E., Im, J.S., Sansano, S., Brando, T., Julien, S., Prandi, J., Gilleron, M., Porcelli, S.A., de la Salle, H., Heck, A.J.R., Mori, L., Puzo, G., Mourey, L., De Libero, G.

To be published.

Macromolecule Content

Total Structure Weight: 96.73 kDa
Atom Count: 6,803
Modelled Residue Count: 750
Deposited Residue Count: 800
Unique protein chains: 2

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	A, C	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
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P29016-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	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 Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	Interactions Focus chain E Focus chain G
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	Interactions Focus chain F
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation	Interactions Focus chain H
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T8X Query on T8X Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain K [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth A]	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		Interactions Focus chain K [auth A] Focus chain Q [auth C]
ULI Query on ULI Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain R [auth C] MOL2 format, chain L [auth A] MOL2 format, chain R [auth C] mmCIF format, chain L [auth A] mmCIF format, chain R [auth C]	L [auth A], R [auth C]	tetracontane C₄₀ H₈₂ KUPLEGDPSCCPJI-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain R [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	I [auth A], O [auth C], P [auth C], S [auth D], T [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth D] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth D]	M [auth B], N [auth B], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A]

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 Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(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
Version 2.2: 2024-10-30
Changes: Structure summary