SAXSdb — 5h5z

▼

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

MHC class I antigen

Ctenopharyngodon idella

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （Q6L7B0） peptide chain × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q65XY8_CTEID
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–275； UniProt 17–291

Beta-2-microglobulin

Ctenopharyngodon idella

UniProt Q6L7B0

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 × 1 （Q65XY8） peptide chain × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6L7B0_CTEID
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–98； UniProt 20–116

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	5h5z
Deposition date deposition_date	2016-11-10
Structure title title	Crystal structure of bony fish MHC class I, peptide and B2m II
Keywords keywords	MHC, IMMUNOLOGY, IMMUNE SYSTEM-TRANSRERASE COMPLEX, PEPTIDE BINDING PROTEIN-IMMUNE SYSTEM complex; PEPTIDE BINDING PROTEIN/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.

5h5z__assembly_1__model_1

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

Download this curve (.dat)

5h5z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5h5z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.55 Å
Rg (electron density)	23.64 Å
Total Rg	24.46 Å
Atom count	3083
Residues	382
Excluded volume	54344 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5h5z__assembly_1__model_1`	trimeric （3）	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	MHC class I antigen
Molecular weight formula_weight	31449.7 kDa
Mutation mutation	E45K
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	3452

GTHSLKYVYTGVSRGIDFPEFTAVGMVDDGQFMYFDSNSMKAVPKTEWIRQNEGADYWDRQTQVLIGAHQVFKDSIQIVMERFNQSKGVHTWQNMYGCELNDDGTTQGFYQYAYDGEDFVSLDKNTLTWTAANPQAVITKHKWEALAVAEQNKGYLENTCIEWLKKYVAYGKDTLERKVSPQVSLLQKDPSSPVTCHATGFYPSGVTITWQKNGQDHDEDVDLGELLPNEDGSFQRMSTLNVGPDEWKNNRFSCVVEHQDKTIRKTEDDIITNFD

Source Source

Source organism organism	Ctenopharyngodon idella
Common name common_name	Grass carp
NCBI taxonomy ID ncbi_taxonomy_id	7959
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11315.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKVSSPKIQVYSHYPGEYGKENTLICYVSNFHPPDISIELLKNGKVIADAQQTDLAFEKGWQFHLTKSVSFKPEKSDEYSCRVKHMSDNKTIVWESNM

Source Source

Source organism organism	Ctenopharyngodon idella
Common name common_name	Grass carp
NCBI taxonomy ID ncbi_taxonomy_id	7959
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	peptide chain
Molecular weight formula_weight	1089.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

FANFCLMMI

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	351

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5h5zA01
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	5h5zA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5h5zB00
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	119.350 Å
Unit-cell length b length_b	50.650 Å
Unit-cell length c length_c	90.310 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	129.37 °
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	1.740 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1727
R_work r_work	0.1710
R_free r_free	0.2045

Crystal structure of bony fish MHC class I, peptide and B2m II

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

MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2-microglobulin

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

5h5z__assembly_1__model_1

5h5z__assembly_1__model_1 | I(q)

5h5z__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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of bony fish MHC class I, peptide and B2m II

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

MHC class I antigen

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5h5z__assembly_1__model_1

5h5z__assembly_1__model_1 | I(q)

5h5z__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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)