6V19

immune receptor complex

PDB DOI: https://doi.org/10.2210/pdb6V19/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Mus musculus
Expression System: Homo sapiens, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-20 Released: 2020-11-25
Deposition Author(s): Lim, J.J., Rossjohn, J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.224
R-Value Work: 0.202
R-Value Observed: 0.203

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: 97.82 kDa
Atom Count: 6,521
Modelled Residue Count: 815
Deposited Residue Count: 851
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, DR alpha chain	A	189	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903 Go to UniProtKB: P01903
PHAROS: P01903 GTEx: ENSG00000204287
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01903
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, DRB1-4 beta chain	B	198	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911 Go to UniProtKB: P01911
PHAROS: P01911 GTEx: ENSG00000196126
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01911
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta 72,74cit69-81	C	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02675 (Homo sapiens) Explore P02675 Go to UniProtKB: P02675
PHAROS: P02675 GTEx: ENSG00000171564
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02675
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
M134 TCR alpha chain	D	209	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
M134 TCR beta chain	E	242	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E]	G [auth A] H [auth B] I [auth D] J [auth D] K [auth D] G [auth A], H [auth B], I [auth D], J [auth D], K [auth D], L [auth D], M [auth E], N [auth E], O [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CIR Query on CIR	C	L-PEPTIDE LINKING	C₆ H₁₃ N₃ O₃		ARG

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.224
R-Value Work: 0.202
R-Value Observed: 0.203
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.462	α = 90
b = 56.848	β = 91.523
c = 129.762	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Lim, J.J.

Rossjohn, J.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE140100011

Revision History (Full details and data files)

Version 1.0: 2020-11-25
Type: Initial release
Version 1.1: 2021-06-09
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations