5nht

human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2

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） Melanoma antigen recognized by T-cells 1 × 1 T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6T6,K7N5N2） T-cell receptor beta variable 19,TRB protein × 1 （A0A0C4ZKA8,A0A5B3） THIOCYANATE ION × 1 POTASSIUM ION × 2 CHLORIDE ION × 1 water × 1	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 H； 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） Melanoma antigen recognized by T-cells 1 × 1 T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6T6,K7N5N2） T-cell receptor beta variable 19,TRB protein × 1 （A0A0C4ZKA8,A0A5B3） THIOCYANATE ION × 1 POTASSIUM ION × 2 CHLORIDE ION × 1 water × 1	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 L； PDBConstruct 2–100； UniProt 21–119

T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain

Homo sapiens

UniProt A0A075B6T6

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） Melanoma antigen recognized by T-cells 1 × 1 T-cell receptor beta variable 19,TRB protein × 1 （A0A0C4ZKA8,A0A5B3） THIOCYANATE ION × 1 POTASSIUM ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A075B6T6_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 2–94； UniProt 21–113

T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain

Homo sapiens

UniProt K7N5N2

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） Melanoma antigen recognized by T-cells 1 × 1 T-cell receptor beta variable 19,TRB protein × 1 （A0A0C4ZKA8,A0A5B3） THIOCYANATE ION × 1 POTASSIUM ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K7N5N2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 95–204； UniProt 96–205

T-cell receptor beta variable 19,TRB protein

Homo sapiens

UniProt A0A0C4ZKA8

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） Melanoma antigen recognized by T-cells 1 × 1 T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6T6,K7N5N2） THIOCYANATE ION × 1 POTASSIUM ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0C4ZKA8_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 100–243； UniProt 31–174

T-cell receptor beta variable 19,TRB protein

Homo sapiens

UniProt A0A5B3

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） Melanoma antigen recognized by T-cells 1 × 1 T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6T6,K7N5N2） THIOCYANATE ION × 1 POTASSIUM ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A5B3_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 2–93； UniProt 22–113

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	5nht
Deposition date deposition_date	2017-03-22
Structure title title	human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2
Keywords keywords	Melan-A/MART-1 PEPTIDE, DECAPEPTIDE, MHC CLASS I, HLA-A2, T cell receptor, 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.

5nht__assembly_1__model_1

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

Download this curve (.dat)

5nht__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nht__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.11 Å
Rg (electron density)	37.30 Å
Total Rg	37.42 Å
Atom count	6612
Residues	825
Excluded volume	115910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nht__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 (9)

Entity 1 Entity 1 polymer

Description description	HLA class I histocompatibility antigen, A-2 alpha chain
Molecular weight formula_weight	31979.4 kDa
Mutation mutation	A245V
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	6613

GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

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	L

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	Melanoma antigen recognized by T-cells 1
Molecular weight formula_weight	985.2 kDa
Mutation mutation	A27L
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ELAGIGILTV

Entity 4 Entity 4 polymer

Description description	T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain
Molecular weight formula_weight	23132.4 kDa
Mutation mutation	T158C,T158C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MQQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVGGGADGLTFGKGTHLIIQPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPENDGGGCK

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 BL21(DE3)

Entity 5 Entity 5 polymer

Description description	T-cell receptor beta variable 19,TRB protein
Molecular weight formula_weight	28292.4 kDa
Mutation mutation	S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSQGLAGAGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADQDRGGGCD

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 BL21(DE3)

Entity 6 Entity 6 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	5nhtA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nhtA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nhtB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nhtB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nhtH01
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	5nhtH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nhtL00
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	222.077 Å
Unit-cell length b length_b	49.284 Å
Unit-cell length c length_c	96.133 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	16.000 Å
R factor r_factor	0.2173
R_work r_work	0.2129
R_free r_free	0.2987

human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2

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 12-2,T-cell receptor, sp3.4 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 12-2,T-cell receptor, sp3.4 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 19,TRB protein

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 19,TRB protein

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

5nht__assembly_1__model_1

5nht__assembly_1__model_1 | I(q)

5nht__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 7 domains