5NQK | pdb_00005nqk

human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2

PDB DOI: https://doi.org/10.2210/pdb5NQK/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-04-20 Released: 2018-05-30
Deposition Author(s): Exertier, C., Reiser, J.-B., Lantez, V., Chouquet, A., Bonneville, M., Saulquin, X., Housset, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free:
0.316 (Depositor), 0.314 (DCC)
R-Value Work:
0.224 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2

Exertier, C., Reiser, J.-B., Housset, D.

To be published.

Macromolecule Content

Total Structure Weight: 96.25 kDa
Atom Count: 6,604
Modeled Residue Count: 825
Deposited Residue Count: 848
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A [auth H]	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439
PHAROS: P04439 GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04439
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 [auth L]	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanoma antigen recognized by T-cells 1	C [auth P]	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16655 (Homo sapiens) Explore Q16655 Go to UniProtKB: Q16655
PHAROS: Q16655 GTEx: ENSG00000120215
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16655
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor alpha variable 12-2,T-cell receptor alpha joining 45,T-cell receptor alpha chain C region	D [auth A]	211	Homo sapiens	Mutation(s): 1 Gene Names: TRAV12-2, TRAJ45, TRAC
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens) Explore P01848 Go to UniProtKB: P01848
PHAROS: P01848
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01848
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor beta variable 19,TRB protein	E [auth B]	251	Homo sapiens	Mutation(s): 0 Gene Names: TCRBV17S1A1T, TRBV19, TRB
UniProt & NIH Common Fund Data Resources
Find proteins for A0A075B6N1 (Homo sapiens) Explore A0A075B6N1 Go to UniProtKB: A0A075B6N1
PHAROS: A0A075B6N1 GTEx: ENSG00000211746
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A075B6N1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.316 (Depositor), 0.314 (DCC)
R-Value Work: 0.224 (Depositor), 0.227 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.18	α = 90
b = 49.72	β = 97.69
c = 95.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary