9OHW | pdb_00009ohw

CD1c presenting GM1 ganglioside

PDB DOI: https://doi.org/10.2210/pdb9OHW/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-05 Released: 2025-11-19
Deposition Author(s): Cao, T.P., Rossjohn, J., Shahine, A.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.247 (Depositor), 0.248 (DCC)
R-Value Work:
0.204 (Depositor), 0.207 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CD1c presenting GM1 ganglioside

Cao, T.P., Rossjohn, J., Shahine, A.

To be published.

Macromolecule Content

Total Structure Weight: 47.04 kDa
Atom Count: 3,311
Modeled Residue Count: 379
Deposited Residue Count: 380
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 CD1c/T-cell surface glycoprotein CD1b chimeric protein	A	281	Homo sapiens	Mutation(s): 0 Gene Names: CD1C
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
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	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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CB7 (Subject of Investigation/LOI) Query on A1CB7 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(2R,3R,4E)-3-hydroxy-2-octadecanamidooctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-[beta-D-galactopyranosyl-(1->3)-2-acetamido-2-deoxy-beta-D-galactopyranosyl-(1->4)]-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside C₇₃ H₁₃₁ N₃ O₃₁ QPJBWNIQKHGLAU-CPBWJLCXSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MK0 Query on MK0 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose C₃₈ H₇₇ O₉ P BWDAWKXFHWFXEQ-RIEBCBCMSA-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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
KZF Query on KZF Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	G [auth A], H [auth A], L [auth B]	2-(cyclohexylazaniumyl)ethanesulfonate C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
GGG Query on GGG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B]	F [auth A], I [auth A], K [auth B]	glycylglycylglycine C₆ H₁₁ N₃ O₄ XKUKSGPZAADMRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B]
MLA Query on MLA 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]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]