SAXSdb — 1qfa

▼

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

PROTEIN (NEUROPEPTIDE Y)

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 52–64	Fragment：NPY Y2 RECEPTOR AGONIST Mutation：I28L, I31L Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 3.6；293 K；Pressure 1 NMR sample composition：40% TFE-D3,60% WATER	Resolution not provided

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 1QFA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RON NMR SOLUTION STRUCTURE OF HUMAN NEUROPEPTIDE Y Deposited 1996-01-11	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–64（36 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.2；310 K	Resolution not provided
7RTA Crystal structures of human PYY and NPY Deposited 2021-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 29–64（36 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Protein complex (~4 mg/mL with respect to Fab, NPY:Fab at molar ratio of 1.4:1, all dissolved in 25 mM Tris (pH 7.5), 100 mM NaCl) was combined to an equal volume (2 uL) of well solution comprising 200 mM Li2SO4, 100 mM sodium acetate (pH 4.5), 22% (w/v) PEG1000	Resolution 2.60 Å R-free 0.270
7VGX Neuropeptide Y Y1 Receptor (NPY1R) in Complex with G Protein and its endogeneous Peptide-Agonist Neuropeptide Y (NPY) Deposited 2021-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 29–64（36 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 3.20 Å
7X9A Cryo-EM structure of neuropeptide Y Y1 receptor in complex with NPY and Gi Deposited 2022-03-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 29–64（36 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7X9B Cryo-EM structure of neuropeptide Y Y2 receptor in complex with NPY and Gi Deposited 2022-03-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 29–64（36 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7YOO Complex structure of Neuropeptide Y Y2 receptor in complex with NPY and Gi Deposited 2022-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 29–64（36 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8K6M Structural complex of neuropeptide Y receptor 1 Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 29–64（36 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8K6N Structural complex of neuropeptide Y receptor 2 Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 29–64（36 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8K6O Structural complex of neuropeptide Y receptor 1 Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 29–64（36 aa）	Mutation：I31L,Q34P	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEUY_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–14； UniProt 52–64

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	1qfa
Deposition date deposition_date	1999-04-08
Structure title title	STRUCTURE OF A NEUROPEPTIDE Y Y2 AGONIST
Keywords keywords	NEUROPEPTIDE Y, AGONIST, HELIX, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	6.62 Å
Radius of gyration Rg (electron density) rg_electron	7.00 Å
Forward intensity I(0) i0	17867700.00
Molecular weight molecular_weight	35823.0 kDa
Excluded volume excluded_volume	45390 Å³
Envelope volume envelope_volume	3886 Å³
Hydration-shell volume shell_volume	4635 Å³
Envelope diameter envelope_diameter	26.1 Å
Shell Rg shell_rg	12.44 Å
Envelope Rg envelope_rg	8.16 Å
Shape Rg shape_rg	6.96 Å
Total Rg total_rg	7.40 Å
Total atoms total_atoms	5220
Residues n_residues	260
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

▼

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

Maximum dimension Dmax dmax	24.8 Å
Rg (real space) rg_real	6.67 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.7870e+07
I(0) uncertainty (real space) i0_real_error	1.7410e+05
Rg (reciprocal space) rg_reciprocal	6.67 Å
I(0) (reciprocal space) i0_reciprocal	17870000.0000
Solution quality estimate total_estimate	0.6677
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	6.9 Å
Skewness Skewness skewness	0.308
Kurtosis Kurtosis kurtosis	-0.627
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	861.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.428; Smooth: 0.802

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1qfaa_
Class class	j — Peptides
Fold Fold fold	j.6 — Peptide hormones
Superfamily Superfamily superfamily	j.6.1 — Peptide hormones
Family Family family	j.6.1.1 — Peptide hormones

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	PROTEIN (NEUROPEPTIDE Y)
Molecular weight formula_weight	1774.1 kDa
Mutation mutation	I28L, I31L
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5220

fit	/app/data/saxs_computation/qf/1qfa/1qfa.fit
pddf	/app/data/pr_computation/qf/1qfa/1qfa.pr.out
profile	/app/data/saxs_computation/qf/1qfa/1qfa.dat

STRUCTURE OF A NEUROPEPTIDE Y Y2 AGONIST

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

PROTEIN (NEUROPEPTIDE Y)

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)