SAXSdb — 6dkp

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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 （Q16655） DMF5 T-cell Receptor Alpha Chain fusion × 1 （A0A075B6T6,P01848） DMF5 T-cell Receptor Beta Chain fusion × 1 （A0A1B0GXE1,K7N5M4）	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 2–276； UniProt 25–299

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 （Q16655） DMF5 T-cell Receptor Alpha Chain fusion × 1 （A0A075B6T6,P01848） DMF5 T-cell Receptor Beta Chain fusion × 1 （A0A1B0GXE1,K7N5M4）	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

Melanoma antigen recognized by T-cells 1

OrganismNot specified

UniProt Q16655

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） DMF5 T-cell Receptor Alpha Chain fusion × 1 （A0A075B6T6,P01848） DMF5 T-cell Receptor Beta Chain fusion × 1 （A0A1B0GXE1,K7N5M4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MAR1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 26–35

DMF5 T-cell Receptor Alpha Chain fusion

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 （Q16655） DMF5 T-cell Receptor Beta Chain fusion × 1 （A0A1B0GXE1,K7N5M4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVAL2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–92； UniProt 23–113

DMF5 T-cell Receptor Alpha Chain fusion

Homo sapiens

UniProt P01848

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 （Q16655） DMF5 T-cell Receptor Beta Chain fusion × 1 （A0A1B0GXE1,K7N5M4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TCA_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 110–200； UniProt 1–91

DMF5 T-cell Receptor Beta Chain fusion

Homo sapiens

UniProt A0A1B0GXE1

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 （Q16655） DMF5 T-cell Receptor Alpha Chain fusion × 1 （A0A075B6T6,P01848）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1B0GXE1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 2–95； UniProt 20–113

DMF5 T-cell Receptor Beta Chain fusion

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） Melanoma antigen recognized by T-cells 1 × 1 （Q16655） DMF5 T-cell Receptor Alpha Chain fusion × 1 （A0A075B6T6,P01848）	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 114–243； UniProt 120–249

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	6dkp
Deposition date deposition_date	2018-05-30
Structure title title	The complex among DMF5(alpha-D26Y, alpha-Y50A,beta-L98W) TCR, human Class I MHC HLA-A2 and MART-1(26-35)(A27L) peptide
Keywords keywords	Alpha-beta T-cell receptor, Class I MHC, HLA-A2, Mart-1 peptide, 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.

6dkp__assembly_1__model_1

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

Download this curve (.dat)

6dkp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6dkp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.98 Å
Rg (electron density)	37.13 Å
Total Rg	37.28 Å
Atom count	6539
Residues	818
Excluded volume	114500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6dkp__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 (5)

Entity 1 Entity 1 polymer

Description description	HLA class I histocompatibility antigen, A-2 alpha chain
Molecular weight formula_weight	31985.4 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	6539

MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

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	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	C

ELAGIGILTV

Entity 4 Entity 4 polymer

Description description	DMF5 T-cell Receptor Alpha Chain fusion
Molecular weight formula_weight	22094.4 kDa
Mutation mutation	D26Y, Y50A,D26Y, Y50A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MKEVEQNSGPLSVPEGAIASLNCTYSYRGSQSFFWYRQYSGKSPELIMFIASNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS

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	DMF5 T-cell Receptor Beta Chain fusion
Molecular weight formula_weight	27132.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MIAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGEVPDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSWSFGTEAFFGQGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

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

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6dkpA01
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	6dkpA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6dkpB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6dkpD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6dkpE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6dkpE02
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	226.485 Å
Unit-cell length b length_b	49.063 Å
Unit-cell length c length_c	92.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.98 °
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	2.966 Å
Low-resolution limit resolution_low	47.943 Å
R factor r_factor	0.2315
R_work r_work	0.2286
R_free r_free	0.2864

The complex among DMF5(alpha-D26Y, alpha-Y50A,beta-L98W) TCR, human Class I MHC HLA-A2 and MART-1(26-35)(A27L) peptide

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

Melanoma antigen recognized by T-cells 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DMF5 T-cell Receptor Alpha Chain fusion

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DMF5 T-cell Receptor Alpha Chain fusion

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DMF5 T-cell Receptor Beta Chain fusion

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DMF5 T-cell Receptor Beta Chain fusion

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

6dkp__assembly_1__model_1

6dkp__assembly_1__model_1 | I(q)

6dkp__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 (5)

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