SAXSdb — 6j2d

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

Ptal-N*01:01

Pteropus alecto

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 （L5K3Y9） HeV1 × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A125R585_PTEAL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–277； UniProt 25–301

beta-2 microglobulin

Pteropus alecto

UniProt L5K3Y9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ptal-N*01:01 × 1 （A0A125R585） HeV1 × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	L5K3Y9_PTEAL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–95； UniProt 187–278

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	6j2d
Deposition date deposition_date	2019-01-01
Structure title title	Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV1
Keywords keywords	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.

6j2d__assembly_1__model_1

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

Download this curve (.dat)

6j2d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6j2d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.11 Å
Rg (electron density)	22.98 Å
Total Rg	23.84 Å
Atom count	3138
Residues	382
Excluded volume	54552 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6j2d__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Ptal-N*01:01
Molecular weight formula_weight	32119.3 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	3222

GFHSLRYFYTAWSRPGSGEPRFVAVGYVDDTQFVRFDSDNASPRAEPRAPWMDLVEQQDPQYWDRNTRNARDAAQTYRVGLDNVRGYYNQSEAGSHTIQRMYGCDVGPHGRLLRGYDQLAYDGADYIALNEDLRSWTAADLAAQNTRRKWEEAGYAERDRAYLEGECVEWLLKHLENGRETLLRADPPKTHITHHPISDREVTLRCWALGFYPEEITLTWQHDGEDQTQEMELVETRPDGNGAFQKWAALVVPSGEEQRYTCHVQHEGLPQPLTLRW

Source Source

Source organism organism	Pteropus alecto
Common name common_name	Black flying fox
NCBI taxonomy ID ncbi_taxonomy_id	9402
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	beta-2 microglobulin
Molecular weight formula_weight	11474.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EPRTPKIQVYSRHPAENGKPNYLNCYVYGFHPPQIEIDLLKNGQKMKTEQSDLSFSKDWSFYLLVHTDFTPSTVDEYSCRVNHSSLAAPHMVKWDRNN

Source Source

Source organism organism	Pteropus alecto
Common name common_name	Black flying fox
NCBI taxonomy ID ncbi_taxonomy_id	9402
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	HeV1
Molecular weight formula_weight	924.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DFANTFLP

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6j2dA01
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	6j2dA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6j2dB00
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	72.458 Å
Unit-cell length b length_b	86.272 Å
Unit-cell length c length_c	134.728 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.313 Å
Low-resolution limit resolution_low	42.828 Å
R factor r_factor	0.2238
R_work r_work	0.2208
R_free r_free	0.2824

Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV1

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

Ptal-N*01:01

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

6j2d__assembly_1__model_1

6j2d__assembly_1__model_1 | I(q)

6j2d__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 bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV1

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

Ptal-N*01:01

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

6j2d__assembly_1__model_1

6j2d__assembly_1__model_1 | I(q)

6j2d__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)