4Z7V

L3-12 complex

PDB DOI: https://doi.org/10.2210/pdb4Z7V/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Triticum aestivum
Expression System: Trichoplusia ni, Escherichia coli BL21
Mutation(s): No

Deposited: 2015-04-08 Released: 2015-06-03
Deposition Author(s): Petersen, J., Rossjohn, J., Reid, H.H., Koning, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.226
R-Value Work: 0.187
R-Value Observed: 0.189

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: 199.19 kDa
Atom Count: 13,077
Modelled Residue Count: 1,615
Deposited Residue Count: 1,742
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ-alpha chain	A, C	192	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DQA1
UniProt
Find proteins for Q30069 (Homo sapiens) Explore Q30069 Go to UniProtKB: Q30069
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q30069
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ-beta-1	B, D	213	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DQB1
UniProt
Find proteins for O19707 (Homo sapiens) Explore O19707 Go to UniProtKB: O19707
Entity Groups
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UniProt Group	O19707
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL RECEPTOR, L3-12 ALPHA CHAIN	E, G	204	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL RECEPTOR, L3-12 BETA CHAIN	F, H	244	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
deamidated DQ8-glia-alpha1 peptide	I, J	18	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for P18573 (Triticum aestivum) Explore P18573 Go to UniProtKB: P18573
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18573
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Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-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	K	6		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G73409CU GlyCosmos: G73409CU GlyGen: G73409CU

Entity ID: 7
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	L	4		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G63564LA GlyCosmos: G63564LA

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 C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth C]	M [auth A], N [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth C] Interactions & Density Focus chain M [auth A] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.226
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.51	α = 93.87
b = 76.961	β = 89.47
c = 132.279	γ = 105.09

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-03
Type: Initial release
Version 1.1: 2015-06-17
Changes: Database references
Version 1.2: 2017-08-23
Changes: Data collection, Derived calculations, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary