3L9R

Crystal structure of bovine CD1b3 with endogenously bound ligands

PDB DOI: https://doi.org/10.2210/pdb3L9R/pdb

Classification: Immune Response
Organism(s): Bos taurus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2010-01-05 Released: 2010-06-16
Deposition Author(s): Zajonc, D.M., Girardi, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.201
R-Value Observed: 0.203

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: 182.01 kDa
Atom Count: 12,721
Modelled Residue Count: 1,490
Deposited Residue Count: 1,524
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD1b3	A, C, E, G	283	Bos taurus	Mutation(s): 0 Gene Names: CD1B3
UniProt
Find proteins for Q1L1H6 (Bos taurus) Explore Q1L1H6 Go to UniProtKB: Q1L1H6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1L1H6
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, F, H	98	Bos taurus	Mutation(s): 0 Gene Names: B2M, beta-2-microglobulin
UniProt
Find proteins for P01888 (Bos taurus) Explore P01888 Go to UniProtKB: P01888
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01888
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)-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	I	6		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G17601US GlyCosmos: G17601US GlyGen: G17601US

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	J, K, L	5		N-Glycosylation	Interactions Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G92953ND GlyCosmos: G92953ND

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L9R Query on L9R Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Y [auth E] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth E]	N [auth A], Y [auth E]	(2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₄ H₈₆ N O₈ P ATHVAWFAEPLPPQ-FLHXZNPISA-N		Interactions Focus chain N [auth A] Focus chain Y [auth E] Interactions & Density Focus chain N [auth A] Focus chain Y [auth E]
L9Q Query on L9Q Download Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain Q [auth C] MOL2 format, chain FA [auth G] MOL2 format, chain Q [auth C]	FA [auth G], Q [auth C]	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₁ H₈₀ N O₈ P JQKOHRZNEOQNJE-VYCVAHKRSA-N		Interactions Focus chain FA [auth G] Focus chain Q [auth C] Interactions & Density Focus chain FA [auth G] Focus chain Q [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain Z [auth G] SDF format, chain P [auth C] MOL2 format, chain M [auth A] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth G] MOL2 format, chain P [auth C]	M [auth A], P [auth C], V [auth E], W [auth E], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain P [auth C] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth G] Interactions & Density Focus chain M [auth A] Focus chain P [auth C] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain O [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth E] SDF format, chain AA [auth G] SDF format, chain U [auth C] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth E] MOL2 format, chain AA [auth G] MOL2 format, chain U [auth C]	AA [auth G] BA [auth G] CA [auth G] DA [auth G] O [auth A] AA [auth G], BA [auth G], CA [auth G], DA [auth G], O [auth A], R [auth C], S [auth C], U [auth C], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain O [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth C] Focus chain X [auth E] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain O [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth C] Focus chain X [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain T [auth C] MOL2 format, chain EA [auth G] MOL2 format, chain T [auth C]	EA [auth G], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth G] Focus chain T [auth C] Interactions & Density Focus chain EA [auth G] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.533	α = 90
b = 139.975	β = 90
c = 111.953	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-16

Deposition Author(s):

Zajonc, D.M.

Girardi, E.

Revision History (Full details and data files)

Version 1.0: 2010-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3L9R

Crystal structure of bovine CD1b3 with endogenously bound ligands

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2