3RUG

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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 CD1d1	A, C	302	Mus musculus	Mutation(s): 0 Gene Names: Cd1d1, Cd1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus) Explore P11609 Go to UniProtKB: P11609
IMPC: MGI:107674
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11609
Sequence Annotations Expand
Reference Sequence

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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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Valpha10(mouse variable domain, human constant domain)	E, G	204	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Vbeta8.1(mouse variable domain, human constant domain)	F, H	241	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J	2		N-Glycosylation	Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DB6 Query on DB6 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth C] MOL2 format, chain K [auth A] MOL2 format, chain N [auth C]	K [auth A], N [auth C]	(11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide C₄₄ H₈₃ N O₉ WSXMIFGRYXQZQZ-IHVNXUITSA-N		Interactions Focus chain K [auth A] Focus chain N [auth C] Interactions & Density Focus chain K [auth A] Focus chain N [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	L [auth A], M [auth A], O [auth C], P [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth C] Focus chain P [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
DB6	Binding MOAD: 3RUG	Kd: 4400 (nM) from 1 assay(s)

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History

Deposition Author(s):

Patel, O.

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2020-01-29
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary