3MBE

TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)

PDB DOI: https://doi.org/10.2210/pdb3MBE/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Gallus gallus
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2010-03-25 Released: 2010-05-12
Deposition Author(s): Corper, A.L., Yoshida, K., Teyton, L., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.281
R-Value Work: 0.253
R-Value Observed: 0.254

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: 203.93 kDa
Atom Count: 13,028
Modelled Residue Count: 1,614
Deposited Residue Count: 1,794
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS II H2-IAg7 ALPHA CHAIN	A, F [auth E]	190	Mus musculus	Mutation(s): 0 Gene Names: H2-Aa
UniProt
Find proteins for P04228 (Mus musculus) Explore P04228 Go to UniProtKB: P04228
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04228
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS II H2-IAg7 BETA CHAIN	B, G [auth F]	201	Mus musculus	Mutation(s): 0 Gene Names: H2-Ab1
UniProt
Find proteins for Q31135 (Mus musculus) Explore Q31135 Go to UniProtKB: Q31135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q31135
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE HEL 11-27	C [auth P], H [auth Q]	18	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR 21.3 alpha chain	D [auth C], I [auth G]	229	Mus musculus	Mutation(s): 0 Gene Names: H2-Ab1
UniProt
Find proteins for P01849 (Mus musculus) Explore P01849 Go to UniProtKB: P01849
Entity Groups
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UniProt Group	P01849
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR 21.3 beta chain	E [auth D], J [auth H]	259	Mus musculus	Mutation(s): 0 Gene Names: H2-Ab1
UniProt
Find proteins for P01852 (Mus musculus) Explore P01852 Go to UniProtKB: P01852
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01852
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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 [auth I], L [auth J]	2		N-Glycosylation	Interactions Focus chain K [auth I] Focus chain L [auth J] Interactions & Density Focus chain K [auth I] Focus chain L [auth J]
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 E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth E]	M [auth A], N [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth E] Interactions & Density Focus chain M [auth A] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.281
R-Value Work: 0.253
R-Value Observed: 0.254
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.468	α = 90
b = 99.391	β = 90
c = 404.677	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
XPREP	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-04-10
Changes: Structure summary
Version 1.3: 2013-05-15
Changes: Database references, Source and taxonomy
Version 1.4: 2018-01-24
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, 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