5KSB

T15-DQ8.5-glia-gamma1 complex

PDB DOI: https://doi.org/10.2210/pdb5KSB/pdb

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

Deposited: 2016-07-08 Released: 2016-09-21
Deposition Author(s): Petersen, J., Rossjohn, J., Reid, H.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.254
R-Value Work: 0.219
R-Value Observed: 0.221

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: 199.43 kDa
Atom Count: 13,106
Modelled Residue Count: 1,623
Deposited Residue Count: 1,752
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, C	191	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens) Explore P01909 Go to UniProtKB: P01909
PHAROS: P01909 GTEx: ENSG00000196735
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01909
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ beta 1 chain	B, D	225	Triticum aestivum, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: HLA-DQB1
UniProt
Find proteins for P08079 (Triticum aestivum) Explore P08079 Go to UniProtKB: P08079
Find proteins for A0A0U5Q247 (Homo sapiens) Explore A0A0U5Q247 Go to UniProtKB: A0A0U5Q247
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P08079A0A0U5Q247
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T15 TCR alpha TRAV20*02	E, G	206	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J274 (Homo sapiens) Explore A0A0B4J274 Go to UniProtKB: A0A0B4J274
PHAROS: A0A0B4J274 GTEx: ENSG00000211800
Find proteins for P01848 (Homo sapiens) Explore P01848 Go to UniProtKB: P01848
PHAROS: P01848
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P01848A0A0B4J274
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T15 TCR beta TRBV9*01	F, H	243	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A580 (Homo sapiens) Explore A0A580 Go to UniProtKB: A0A580
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9 Go to UniProtKB: A0A5B9
PHAROS: A0A5B9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	A0A580A0A5B9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DQ8.5-glia-gamma1 peptide	I, J	11	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for P08079 (Triticum aestivum) Explore P08079 Go to UniProtKB: P08079
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08079
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L	2		N-Glycosylation	Interactions Focus chain K Focus chain L Interactions & Density Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D]	M [auth A], N [auth B], O [auth C], P [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.254
R-Value Work: 0.219
R-Value Observed: 0.221
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.89	α = 90
b = 125.05	β = 90
c = 165.63	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Petersen, J.

Rossjohn, J.

Reid, H.H.

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2016-10-19
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary