6BMK

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d2	A, C	276	Mus musculus	Mutation(s): 0 Gene Names: Cd1d2, Cd1.2
UniProt
Find proteins for P11610 (Mus musculus) Explore P11610 Go to UniProtKB: P11610
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11610
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, D	99	Mus musculus	Mutation(s): 0 Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887 Go to UniProtKB: P01887
IMPC: MGI:88127
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F57 Query on F57 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth C]	H [auth A], J [auth C]	(2R)-1-(decanoyloxy)-3-(phosphonooxy)propan-2-yl octadecanoate C₃₁ H₆₁ O₈ P NEHFRILYYHJEFJ-GDLZYMKVSA-N		Interactions Focus chain H [auth A] Focus chain J [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C]	G [auth A], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain I [auth C] Interactions & Density Focus chain G [auth A] Focus chain I [auth C]

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History

Deposition Author(s):

Khandokar, Y.B.

Version 1.0: 2018-01-31
Type: Initial release
Version 1.1: 2018-02-21
Changes: Database references
Version 2.0: 2018-03-07
Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-10-04
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary