8GLH

Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5

PDB DOI: https://doi.org/10.2210/pdb8GLH/pdb

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

Deposited: 2023-03-22 Released: 2023-09-20
Deposition Author(s): Farquhar, R., Rossjohn, J., Shahine, A.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.221
R-Value Work: 0.166
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms

Huang, S., Shahine, A., Cheng, T.Y., Chen, Y.L., Ng, S.W., Balaji, G.R., Farquhar, R., Gras, S., Hardman, C.S., Altman, J.D., Tahiri, N., Minnaard, A.J., Ogg, G.S., Mayfield, J.A., Rossjohn, J., Moody, D.B.

(2023) Cell 186: 1-14

DOI: https://doi.org/10.1016/j.cell.2023.08.022

Macromolecule Content

Total Structure Weight: 49.36 kDa
Atom Count: 3,660
Modelled Residue Count: 380
Deposited Residue Count: 401
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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	101	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

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)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G92953ND GlyCosmos: G92953ND

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3IY (Subject of Investigation/LOI) Query on 3IY Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	[(2~{R})-1-dodecanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] (8~{Z},11~{Z},14~{Z},24~{Z},27~{Z})-triaconta-8,11,14,24,27-pentaenoate C₅₀ H₉₁ N O₈ P JZJDDTSQGYPVAU-XFFLUJDDSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
3IV (Subject of Investigation/LOI) Query on 3IV Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	(11E)-hexadec-11-enoic acid C₁₆ H₃₀ O₂ JGMYDQCXGIMHLL-AATRIKPKSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B]	E [auth A], L [auth B], N [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain N [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]