3U0P

Crystal structure of human CD1d-lysophosphatidylcholine

PDB DOI: https://doi.org/10.2210/pdb3U0P/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2011-09-28 Released: 2012-04-25
Deposition Author(s): Lopez-Sagaseta, J., Sibener, L.V., Adams, E.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.259
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 137.96 kDa
Atom Count: 8,971
Modelled Residue Count: 1,056
Deposited Residue Count: 1,158
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	A, C, E	284	Homo sapiens	Mutation(s): 3 Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens) Explore P15813 Go to UniProtKB: P15813
PHAROS: P15813 GTEx: ENSG00000158473
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15813
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, D, F	102	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

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G63564LA GlyCosmos: G63564LA

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G04836KE GlyCosmos: G04836KE GlyGen: G04836KE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	2		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LSC Query on LSC Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain T [auth C] MOL2 format, chain J [auth A] MOL2 format, chain T [auth C]	J [auth A], T [auth C]	(4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide C₂₆ H₅₃ N O₇ P YAMUFBLWGFFICM-ZOGNMOHXSA-O		Interactions Focus chain J [auth A] Focus chain T [auth C] Interactions & Density Focus chain J [auth A] Focus chain T [auth C]
UND Query on UND Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A]	Q [auth A]	UNDECANE C₁₁ H₂₄ RSJKGSCJYJTIGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain M [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] SDF format, chain AA [auth D] SDF format, chain FA [auth F] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth C]	AA [auth D] CA [auth D] FA [auth F] L [auth A] M [auth A] AA [auth D], CA [auth D], FA [auth F], L [auth A], M [auth A], N [auth A], U [auth C], V [auth C], W [auth C], Y [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain FA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain FA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth C] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain X [auth C] SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B]	BA [auth D] DA [auth D] O [auth A] P [auth A] R [auth B] BA [auth D], DA [auth D], O [auth A], P [auth A], R [auth B], S [auth B], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
NBU Query on NBU Download Ideal Coordinates CCD File SDF format, chain EA [auth E] MOL2 format, chain EA [auth E]	EA [auth E]	N-BUTANE C₄ H₁₀ IJDNQMDRQITEOD-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Interactions & Density Focus chain EA [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
LSC	PDBBind: 3U0P	Kd: 2100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.259
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.609	α = 90
b = 127.189	β = 90
c = 332.641	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Lopez-Sagaseta, J.

Sibener, L.V.

Adams, E.J.

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2017-11-08
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3U0P

Crystal structure of human CD1d-lysophosphatidylcholine

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)