6V7Y | pdb_00006v7y

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5

PDB DOI: https://doi.org/10.2210/pdb6V7Y/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2019-12-10 Released: 2020-09-16
Deposition Author(s): Shahine, A., Rossjohn, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.276 (Depositor), 0.240 (DCC)
R-Value Work:
0.241 (Depositor)
R-Value Observed:
0.201 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.

Shahine, A., Rossjohn, J.

(2020) Nat Cancer

DOI: https://doi.org/10.1038/s43018-020-00111-6

Macromolecule Content

Total Structure Weight: 68.11 kDa
Atom Count: 4,324
Modeled Residue Count: 496
Deposited Residue Count: 574
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	A	347	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15813
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A	Go to GlyGen: P15813-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH ID5	C [auth F]	127	Lama glama	Mutation(s): 0

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D]	3		N-Glycosylation	Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGH (Subject of Investigation/LOI) Query on AGH Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE C₅₀ H₉₉ N O₉ VQFKFAKEUMHBLV-BYSUZVQFSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A]	F [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A], L [auth A], M [auth A], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.276 (Depositor), 0.240 (DCC)
R-Value Work: 0.241 (Depositor)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.27	α = 90
b = 73.27	β = 90
c = 261.077	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Shahine, A.

Rossjohn, J.

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

6V7Y | pdb_00006v7y

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5

Literature

A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Oligosaccharides

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)