6r2l

NYBR1-A2-SLSKILDTV

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

HLA class I histocompatibility antigen, A-2 alpha chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL × 1 T cell receptor alpha variable 22,Human nkt tcr alpha chain × 1 （A0A0B4J277,K7N5M3） T cell receptor beta variable 11-2,Human nkt tcr beta chain × 1 （A0A584,K7N5M4） DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 2 GLYCEROL × 3 SULFATE ION × 8 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	1A02_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 25–300

Beta-2-microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, A-2 alpha chain × 1 （P01892） SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL × 1 T cell receptor alpha variable 22,Human nkt tcr alpha chain × 1 （A0A0B4J277,K7N5M3） T cell receptor beta variable 11-2,Human nkt tcr beta chain × 1 （A0A584,K7N5M4） DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 2 GLYCEROL × 3 SULFATE ION × 8 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–100； UniProt 21–119

T cell receptor alpha variable 22,Human nkt tcr alpha chain

Homo sapiens

UniProt A0A0B4J277

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, A-2 alpha chain × 1 （P01892） Beta-2-microglobulin × 1 （P61769） SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL × 1 T cell receptor beta variable 11-2,Human nkt tcr beta chain × 1 （A0A584,K7N5M4） DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 2 GLYCEROL × 3 SULFATE ION × 8 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVA22_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–90； UniProt 21–109

T cell receptor alpha variable 22,Human nkt tcr alpha chain

Homo sapiens

UniProt K7N5M3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, A-2 alpha chain × 1 （P01892） Beta-2-microglobulin × 1 （P61769） SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL × 1 T cell receptor beta variable 11-2,Human nkt tcr beta chain × 1 （A0A584,K7N5M4） DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 2 GLYCEROL × 3 SULFATE ION × 8 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K7N5M3_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 114–194； UniProt 118–198

T cell receptor beta variable 11-2,Human nkt tcr beta chain

Homo sapiens

UniProt A0A584

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, A-2 alpha chain × 1 （P01892） Beta-2-microglobulin × 1 （P61769） SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL × 1 T cell receptor alpha variable 22,Human nkt tcr alpha chain × 1 （A0A0B4J277,K7N5M3） DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 2 GLYCEROL × 3 SULFATE ION × 8 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVBK2_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–94； UniProt 21–114

T cell receptor beta variable 11-2,Human nkt tcr beta chain

Homo sapiens

UniProt K7N5M4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, A-2 alpha chain × 1 （P01892） Beta-2-microglobulin × 1 （P61769） SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL × 1 T cell receptor alpha variable 22,Human nkt tcr alpha chain × 1 （A0A0B4J277,K7N5M3） DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 2 GLYCEROL × 3 SULFATE ION × 8 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K7N5M4_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 105–247； UniProt 107–249

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6r2l
Deposition date deposition_date	2019-03-18
Structure title title	NYBR1-A2-SLSKILDTV
Keywords keywords	;NYBR1, TCR, HLA-A*0201, A2, HLA-A2, MHC-I, cancer, NY-BR-1, breast cancer, high affinity TCR, immunotherapy, T-cell, 3D Structure, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6r2l__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6r2l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6r2l__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	38.20 Å
Rg (electron density)	38.37 Å
Total Rg	38.53 Å
Atom count	6742
Residues	826
Excluded volume	118170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6r2l__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	HLA class I histocompatibility antigen, A-2 alpha chain
Molecular weight formula_weight	31951.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7152

GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11879.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL
Molecular weight formula_weight	976.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SLSKILDTV

Entity 4 Entity 4 polymer

Description description	T cell receptor alpha variable 22,Human nkt tcr alpha chain
Molecular weight formula_weight	21676.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGIQVEQSPPDLILQEGANSTLRCNFSDSVNNLQWFHQNPWGQLINLFYIPSGWKQEGRLSATTVATERYSLLYISSSQTTDSGVYFCAVGGNDWNTDKLIFGTGTRLQVFPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSII

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	T cell receptor beta variable 11-2,Human nkt tcr beta chain
Molecular weight formula_weight	27893.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

AGVAQSPRYKIIEKRQSVAFWCNPIFSHPTLYWYQQILGQGPKLLIQFGGWPGVDDSQLPKDRFSAERLKGVDSTLKIQPAKLEDSALYLCASSPLDVSISSYNEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 10 Entity 10 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6r2lA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	6r2lA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6r2lB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6r2lE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	52.210 Å
Unit-cell length b length_b	99.330 Å
Unit-cell length c length_c	111.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	52.210 Å
R factor r_factor	0.2168
R_work r_work	0.2143
R_free r_free	0.2650

NYBR1-A2-SLSKILDTV

1. Protein Identity and Related Structures Protein Identity & Related Structures

HLA class I histocompatibility antigen, A-2 alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor alpha variable 22,Human nkt tcr alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor alpha variable 22,Human nkt tcr alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor beta variable 11-2,Human nkt tcr beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor beta variable 11-2,Human nkt tcr beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6r2l__assembly_1__model_1

6r2l__assembly_1__model_1 | I(q)

6r2l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer