SAXSdb — 6ilf

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

MHC class I antigen

Pteropus alecto

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 25–303	Fragment：UNP residues 25-303	Beta-2-microglobulin × 1 HEV-2 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 6.5, 25%(w/v) Polyethylene glycol 3,350	Resolution 2.70 Å R-free 0.292

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6ILF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ILC CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.2 ANGSTROM Deposited 2018-10-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–303（279 aa） Fragment：UNP residues 25-303	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS ph6.5, 25%(w/v) Polyethylene glycol 3,350	Resolution 2.20 Å R-free 0.230
6ILE CRYSTAL STRUCTURE OF A MUTANT PTAL-N*01:01 FOR 2.9 ANGSTROM, 52M 53D 54L DELETED Deposited 2018-10-17	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–303（279 aa） Fragment：UNP residues 25-303	Mutation：52M, 53D, 54L deleted	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dehydrate pH 5.6 and 30%(w/v) polyethylene glycol 4,000	Resolution 2.90 Å R-free 0.293
6ILG CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.6 ANGSTROM Deposited 2018-10-18	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–303（279 aa） Fragment：UNP residues 25-303	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 6.5, 25%(w/v) Polyethylene glycol 3,350	Resolution 2.60 Å R-free 0.276
6J2D Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV1 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), and 25% (w/v) polyethylene glycol 3,350 at a concentration of 7.5 mg/mL.	Resolution 2.31 Å R-free 0.282
6J2E Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola virus-derived peptide EBOV-NP1 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M succinic acid pH 7.0, 15%(w/v) polyethylene glycol 3,350	Resolution 2.10 Å R-free 0.257
6J2E Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola virus-derived peptide EBOV-NP1 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M succinic acid pH 7.0, 15%(w/v) polyethylene glycol 3,350	Resolution 2.10 Å R-free 0.257
6J2F Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV2 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.075 M HEPES (pH 7.5), 15% (w/v) polyethylene glycol 10,000, and 25% (v/v) glycerol at a protein concentration of 10 mg/mL. Single crystals of Ptal-N*01:01/ EBOV-NP1 were grown in 0.1 M succinic acid pH 7.0, 15% w/v polyethylene glycol 3,350.	Resolution 1.90 Å R-free 0.231
6J2F Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV2 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.075 M HEPES (pH 7.5), 15% (w/v) polyethylene glycol 10,000, and 25% (v/v) glycerol at a protein concentration of 10 mg/mL. Single crystals of Ptal-N*01:01/ EBOV-NP1 were grown in 0.1 M succinic acid pH 7.0, 15% w/v polyethylene glycol 3,350.	Resolution 1.90 Å R-free 0.231
6J2G Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola virus-derived peptide EBOV-NP2 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M ammonium acetate, 0.1 M Tris pH 8.0, 16% w/v polyethylene glycol 10,000	Resolution 2.41 Å R-free 0.233
6J2G Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola virus-derived peptide EBOV-NP2 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M ammonium acetate, 0.1 M Tris pH 8.0, 16% w/v polyethylene glycol 10,000	Resolution 2.41 Å R-free 0.233
6J2H Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 mutant (Met52 Asp53 Leu54 deleted) in complex with Hendra virus-derived peptide HeV1 Deposited 2019-01-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Mutation：52-54 deletion	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M sodium formate, 20%(w/v) polyethylene glycol 3,350	Resolution 2.30 Å R-free 0.228
6J2H Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 mutant (Met52 Asp53 Leu54 deleted) in complex with Hendra virus-derived peptide HeV1 Deposited 2019-01-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–301（277 aa）	Mutation：52-54 deletion	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M sodium formate, 20%(w/v) polyethylene glycol 3,350	Resolution 2.30 Å R-free 0.228
6J2I Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with H17N10 influenza-like virus-derivrd peptide H17N10-NP Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.075 M HEPES pH 7.5, 15% w/v polyethylene glycol 10,000, 25% v/v glycerol.	Resolution 2.30 Å R-free 0.253
6J2I Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with H17N10 influenza-like virus-derivrd peptide H17N10-NP Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.075 M HEPES pH 7.5, 15% w/v polyethylene glycol 10,000, 25% v/v glycerol.	Resolution 2.30 Å R-free 0.253
6J2J Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with MERS-CoV-derived peptide MERS-CoV-S3 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350	Resolution 2.50 Å R-free 0.267
6J2J Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with MERS-CoV-derived peptide MERS-CoV-S3 Deposited 2019-01-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350	Resolution 2.50 Å R-free 0.267
6K7T Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV1--human beta-2 microglobulin Deposited 2019-06-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–301（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.0, 2% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.234

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A125R585_PTEAL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–279； UniProt 25–303

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	6ilf
Deposition date deposition_date	2018-10-17
Structure title title	CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.7 ANGSTROM
Keywords keywords	IMMUNOLOGY, VIRUS, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.14 Å
Radius of gyration Rg (electron density) rg_electron	23.02 Å
Forward intensity I(0) i0	36973200.00
Molecular weight molecular_weight	44731.0 kDa
Excluded volume excluded_volume	54987 Å³
Envelope volume envelope_volume	67956 Å³
Hydration-shell volume shell_volume	24743 Å³
Envelope diameter envelope_diameter	78.8 Å
Shell Rg shell_rg	29.73 Å
Envelope Rg envelope_rg	23.13 Å
Shape Rg shape_rg	22.99 Å
Total Rg total_rg	23.89 Å
Total atoms total_atoms	3164
Residues n_residues	386
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	75.3 Å
Rg (real space) rg_real	24.08 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.6970e+07
I(0) uncertainty (real space) i0_real_error	5.0420e+05
Rg (reciprocal space) rg_reciprocal	24.09 Å
I(0) (reciprocal space) i0_reciprocal	36970000.0000
Solution quality estimate total_estimate	0.9094
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9820000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	MHC class I antigen
Molecular weight formula_weight	32345.5 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	3175

GFHSLRYFYTAWSRPGSGEPRFVAVGYVDDTQFVRFDSDNASPRAEPRAPWMDLVEQQDPQYWDRNTRNARDAAQTYRVGLDNVRGYYNQSEAGSHTIQRMYGCDVGPHGRLLRGYDQLAYDGADYIALNEDLRSWTAADLAAQNTRRKWEEAGYAERDRAYLEGECVEWLLKHLENGRETLLRADPPKTHITHHPISDREVTLRCWALGFYPEEITLTWQHDGEDQTQEMELVETRPDGNGAFQKWAALVVPSGEEQRYTCHVQHEGLPQPLTLRWEP

来源 Source

来源生物 organism	Pteropus alecto
通用名 common_name	Black flying fox
NCBI Class编号 ncbi_taxonomy_id	9402
宿主生物 host_organism	Escherichia coli

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

来源 Source

来源生物 organism	Pteropus alecto
通用名 common_name	Black flying fox
NCBI Class编号 ncbi_taxonomy_id	9402
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	HEV-2
Molecular weight formula_weight	1048.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DYINTNLVP

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6ilfA01
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	6ilfA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6ilfB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	72.126 Å
Unit-cell length b length_b	87.871 Å
Unit-cell length c length_c	133.992 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	2.700 Å
Low-resolution limit resolution_low	28.713 Å
R factor r_factor	0.2190
R_work r_work	0.2153
R_free r_free	0.2925

fit	/app/data/saxs_computation/il/6ilf/6ilf.fit
pddf	/app/data/pr_computation/il/6ilf/6ilf.pr.out
profile	/app/data/saxs_computation/il/6ilf/6ilf.dat

CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.7 ANGSTROM

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)