1mhc

MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION

▼

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

MHC CLASS I ANTIGEN H2-M3

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC CLASS I ANTIGEN H2-M3 × 1 （P01887） NONAPEPTIDE FROM RAT NADH DEHYDROGENASE × 1 （P03889） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	MHC CLASS I ANTIGEN H2-M3 × 1 （P01887） NONAPEPTIDE FROM RAT NADH DEHYDROGENASE × 1 （P03889） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	MHC CLASS I ANTIGEN H2-M3 × 2 （P01887） NONAPEPTIDE FROM RAT NADH DEHYDROGENASE × 2 （P03889） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q31093_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 25–298 Author chain D； PDBConstruct 1–276； UniProt 25–298

MHC CLASS I ANTIGEN H2-M3

Mus musculus

UniProt P01887

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC CLASS I ANTIGEN H2-M3 × 1 （Q31093） NONAPEPTIDE FROM RAT NADH DEHYDROGENASE × 1 （P03889） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	MHC CLASS I ANTIGEN H2-M3 × 1 （Q31093） NONAPEPTIDE FROM RAT NADH DEHYDROGENASE × 1 （P03889） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	MHC CLASS I ANTIGEN H2-M3 × 2 （Q31093） NONAPEPTIDE FROM RAT NADH DEHYDROGENASE × 2 （P03889） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 21–119 Author chain E； PDBConstruct 1–99； UniProt 21–119

NONAPEPTIDE FROM RAT NADH DEHYDROGENASE

Rattus rattus

UniProt P03889

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC CLASS I ANTIGEN H2-M3 × 1 （Q31093） MHC CLASS I ANTIGEN H2-M3 × 1 （P01887） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	MHC CLASS I ANTIGEN H2-M3 × 1 （Q31093） MHC CLASS I ANTIGEN H2-M3 × 1 （P01887） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	MHC CLASS I ANTIGEN H2-M3 × 2 （Q31093） MHC CLASS I ANTIGEN H2-M3 × 2 （P01887） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU1M_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–9； UniProt 1–9 Author chain F； PDBConstruct 1–9； UniProt 1–9

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	1mhc
Deposition date deposition_date	1995-08-23
Structure title title	MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION
Keywords keywords	HISTOCOMPATIBILITY ANTIGEN/PEPTIDE, HISTOCOMPATIBILITY ANTIGEN-PEPTIDE complex; HISTOCOMPATIBILITY ANTIGEN/PEPTIDE
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.

1mhc__assembly_1__model_1

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

Download this curve (.dat)

1mhc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mhc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.25 Å
Rg (electron density)	23.23 Å
Total Rg	24.14 Å
Atom count	3141
Residues	383
Excluded volume	55510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mhc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1mhc__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1mhc__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MHC CLASS I ANTIGEN H2-M3
Molecular weight formula_weight	32650.7 kDa
Mutation mutation	INS(275(A)-282(A)), INS(275(D)-282(D))
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	6668

GSHSLRYFHTAVSRPGRGEPQYISVGYVDDVQFQRCDSIEEIPRMEPRAPWMEKERPEYWKELKLKVKNIAQSARANLRTLLRYYNQSEGGSHILQWMVSCEVGPDMRLLGAHYQAAYDGSDYITLNEDLSSWTAVDMVSQITKSRLESAGTAEYFRAYVEGECLELLHRFLRNGKEILQRADPPKAHVAHHPRPKGDVTLRCWALGFYPADITLTWQKDEEDLTQDMELVETRPSGDGTFQKWAAVVVPSGEEQRYTCYVHHEGLTEPLALKWRSHHHHHH

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	MHC CLASS I ANTIGEN H2-M3
Molecular weight formula_weight	11704.4 kDa
Mutation mutation	INS(275(A)-282(A)), INS(275(D)-282(D))
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Drosophila melanogaster

Entity 3 Entity 3 polymer

Description description	NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
Molecular weight formula_weight	1155.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MYFINILTL

Source Source

Source organism organism	Rattus rattus
Common name common_name	black rat
NCBI taxonomy ID ncbi_taxonomy_id	10117

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	372

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1mhca1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1mhca2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d1mhcb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1mhcd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1mhcd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d1mhce_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	1mhcA01
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	1mhcA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1mhcB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1mhcD01
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	1mhcD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1mhcE00
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	65.250 Å
Unit-cell length b length_b	66.100 Å
Unit-cell length c length_c	55.170 Å
Unit-cell angle α angle_alpha	102.71 °
Unit-cell angle β angle_beta	96.28 °
Unit-cell angle γ angle_gamma	110.19 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	—

MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION

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

MHC CLASS I ANTIGEN H2-M3

State in the Current Structure

Other States of the Same Protein in the Database

MHC CLASS I ANTIGEN H2-M3

State in the Current Structure

Other States of the Same Protein in the Database

NONAPEPTIDE FROM RAT NADH DEHYDROGENASE

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

1mhc__assembly_1__model_1

1mhc__assembly_1__model_1 | I(q)

1mhc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION

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

MHC CLASS I ANTIGEN H2-M3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

MHC CLASS I ANTIGEN H2-M3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NONAPEPTIDE FROM RAT NADH DEHYDROGENASE

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

1mhc__assembly_1__model_1

1mhc__assembly_1__model_1 | I(q)

1mhc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)