SAXSdb — 6mkd

▼

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

H-2 class II histocompatibility antigen, A-B alpha chain

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain × 1 （P14483,Q9Z183） 4699 TCR alpha chain × 1 4699 TCR beta chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HA2B_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–179； UniProt 27–205

Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain

Mus musculus

UniProt P14483

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	H-2 class II histocompatibility antigen, A-B alpha chain × 1 （P14434） 4699 TCR alpha chain × 1 4699 TCR beta chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HB2A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 29–217； UniProt 30–218

Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain

Mus musculus

UniProt Q9Z183

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	H-2 class II histocompatibility antigen, A-B alpha chain × 1 （P14434） 4699 TCR alpha chain × 1 4699 TCR beta chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PADI4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–13； UniProt 93–105

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6mkd
Deposition date deposition_date	2018-09-25
Structure title title	4699 TCR bound to I-Ab Padi4
Keywords keywords	T cell receptor, Major Histocompatibility Complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6mkd__assembly_1__model_1

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

Download this curve (.dat)

6mkd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6mkd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.33 Å
Rg (electron density)	36.66 Å
Total Rg	36.84 Å
Atom count	5916
Residues	799
Excluded volume	103360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6mkd__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	H-2 class II histocompatibility antigen, A-B alpha chain
Molecular weight formula_weight	20242.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	5916

IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain
Molecular weight formula_weight	25027.9 kDa
EC 编号 ec_number	3.5.3.15
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

RVSYYGPKTSPVQGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	4699 TCR alpha chain
Molecular weight formula_weight	23230.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MQQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLIAIRSVSDKKEDGRFTIFFNKREKKLSLHITDSQPGDSATYFCAASDTGANTGKLTFGHGTILRVHPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	4699 TCR beta chain
Molecular weight formula_weight	26756.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

▼

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	6mkdA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mkdB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mkdB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6mkdC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	6mkdC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

Unit-cell length a length_a	255.448 Å
Unit-cell length b length_b	73.643 Å
Unit-cell length c length_c	64.566 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.39 °
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	29.242 Å
R factor r_factor	0.2351
R_work r_work	0.2329
R_free r_free	0.2779

4699 TCR bound to I-Ab Padi4

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

H-2 class II histocompatibility antigen, A-B alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6mkd__assembly_1__model_1

6mkd__assembly_1__model_1 | I(q)

6mkd__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 (4)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

4699 TCR bound to I-Ab Padi4

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

H-2 class II histocompatibility antigen, A-B 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

Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A 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

Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A 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

6mkd__assembly_1__model_1

6mkd__assembly_1__model_1 | I(q)

6mkd__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 (4)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)