5L2J

Crystal Structure of human CD1b in complex with C36-GMM

PDB DOI: https://doi.org/10.2210/pdb5L2J/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2016-08-02 Released: 2016-11-16
Deposition Author(s): Gras, S., Shahine, A., Le Nours, J., Rossjohn, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.199
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 48.09 kDa
Atom Count: 3,618
Modelled Residue Count: 377
Deposited Residue Count: 398
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1b	A	300	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	98	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

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Entity ID: 3
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-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G11460AB GlyCosmos: G11460AB GlyGen: G11460AB

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
70E Query on 70E Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose C₄₂ H₈₂ O₈ YOCZDGRJDQLKHW-GWLFWXKWSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
6UL Query on 6UL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	TETRACOSYL PALMITATE C₄₀ H₈₀ O₂ KKTAIMZGSAQXRE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.199
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.66	α = 90
b = 78.11	β = 90
c = 91.33	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-16
Type: Initial release
Version 1.1: 2016-12-07
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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5L2J

Crystal Structure of human CD1b in complex with C36-GMM

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2