SAXSdb — 5zbq

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

Neuropeptide Y receptor type 1,T4 Lysozyme

Enterobacteria phage RB55

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–161	Fragment：UNP residues 2-358,UNP residues 2-161 Mutation：F129W,C1053T, C1096A	9AO N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 7.4；293 K；0.1 M Tris, pH 7.4-8.0, 30-40% (v/v) PEG400, 50-150 mM sodium tartrate and 100 uM UR-MK299	Resolution 2.70 Å R-free 0.247

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 5ZBQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5W0P Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser Deposited 2017-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–161（160 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5；293 K；PEG 400, magnesium acetate, sodium acetate.	Resolution 3.01 Å R-free 0.272
5W0P Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser Deposited 2017-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–161（160 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5；293 K；PEG 400, magnesium acetate, sodium acetate.	Resolution 3.01 Å R-free 0.272
5W0P Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser Deposited 2017-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–161（160 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5；293 K；PEG 400, magnesium acetate, sodium acetate.	Resolution 3.01 Å R-free 0.272
5W0P Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser Deposited 2017-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–161（160 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5；293 K；PEG 400, magnesium acetate, sodium acetate.	Resolution 3.01 Å R-free 0.272
5X33 Leukotriene B4 receptor BLT1 in complex with BIIL260 Deposited 2017-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–161（160 aa）	Mutation：H83G,K88G,V212A,C1054T,C1097A,S102A	7Y9 4-[[3-[[4-[2-(4-hydroxyphenyl)propan-2-yl]phenoxy]methyl]phenyl]methoxy]benzenecarboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；277 K；PEG 300, Bicine	Resolution 3.70 Å R-free 0.296

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A097J792_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 366–525； UniProt 2–161

Neuropeptide Y receptor type 1,T4 Lysozyme

Enterobacteria phage RB55

UniProt P25929

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–358	Fragment：UNP residues 2-358,UNP residues 2-161 Mutation：F129W,C1053T, C1096A	9AO N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 7.4；293 K；0.1 M Tris, pH 7.4-8.0, 30-40% (v/v) PEG400, 50-150 mM sodium tartrate and 100 uM UR-MK299	Resolution 2.70 Å R-free 0.247

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 5ZBQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5ZBH The Crystal Structure of Human Neuropeptide Y Y1 Receptor with BMS-193885 Deposited 2018-02-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–241（240 aa） Fragment：UNP residues 2-241,UNP residues 2-161,UNP residues 250-358 Chain A 250–358（109 aa） Fragment：UNP residues 2-241,UNP residues 2-161,UNP residues 250-358	Mutation：F129W,C1053T, C1096A Mutation：F129W,C1053T, C1096A	9AF dimethyl 4-{3-[({3-[4-(3-methoxyphenyl)piperidin-1-yl]propyl}carbamoyl)amino]phenyl}-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.4；293 K；0.1M HEPES, pH 7.2-7.6, 20% PEG400	Resolution 3.00 Å R-free 0.251
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–384（384 aa）	Not recorded	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–340（340 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
8K6M Structural complex of neuropeptide Y receptor 1 Deposited 2023-07-25	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 × 6 PDB declaration: hexameric	Chain D 1–349（349 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
8K6O Structural complex of neuropeptide Y receptor 1 Deposited 2023-07-25	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 × 6 PDB declaration: hexameric	Chain D 1–341（341 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NPY1R_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–357； UniProt 2–358

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	5zbq
Deposition date deposition_date	2018-02-12
Structure title title	The Crystal Structure of human neuropeptide Y Y1 receptor with UR-MK299
Keywords keywords	G Protein-Coupled Receptor, Receptor Inhibitor, Complex structure, SIGNALING PROTEIN; SIGNALING PROTEIN
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	31.38 Å
Radius of gyration Rg (electron density) rg_electron	30.66 Å
Forward intensity I(0) i0	40858000.00
Molecular weight molecular_weight	53305.0 kDa
Excluded volume excluded_volume	68111 Å³
Envelope volume envelope_volume	88923 Å³
Hydration-shell volume shell_volume	25982 Å³
Envelope diameter envelope_diameter	113.1 Å
Shell Rg shell_rg	35.23 Å
Envelope Rg envelope_rg	30.59 Å
Shape Rg shape_rg	30.67 Å
Total Rg total_rg	31.13 Å
Total atoms total_atoms	3760
Residues n_residues	463
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	108.2 Å
Rg (real space) rg_real	31.67 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	4.0860e+07
I(0) uncertainty (real space) i0_real_error	5.7960e+05
Rg (reciprocal space) rg_reciprocal	31.55 Å
I(0) (reciprocal space) i0_reciprocal	40850000.0000
Solution quality estimate total_estimate	0.8295
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.432
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8590000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.734; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.659; Smooth: 0.919

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Neuropeptide Y receptor type 1,T4 Lysozyme
Molecular weight formula_weight	60595.2 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	F129W,C1053T, C1096A
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	3760

NSTLFSQVENHSVHSNFSEKNAQLLAFENDDCHLPLAMIFTLALAYGAVIILGVSGNLALIIIILKQKEMRNVTNILIVNLSFSDLLVAIMCLPFTFVYTLMDHWVFGEAMCKLNPFVQCVSITVSIWSLVLIAVERHQLIINPRGWRPNNRHAYVGIAVIWVLAVASSLPFLIYQVMTDEPFQNVTLDAYKDKYVCFDQFPSDSHRLSYTTLLLVLQYFGPLCFIFICYFKIYIRLKRRNNMMDKMRDNKYRSSETKRINIMLLSIVVAFAVCWLPLTIFNTVFDWNHQIIATCNHNLLFLLCHLTAMISTCVNPIFYGFLNKNFQRDLQFFFNFCDFRSRDDDYETIAMSTMHTDEFLEVLFQNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAY

来源 Source

来源生物 organism	Enterobacteria phage RB55
NCBI Class编号 ncbi_taxonomy_id	697289
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide
Molecular weight formula_weight	615.7 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5zbqA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

Domain ID domain_id	5zbqA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	37.840 Å
Unit-cell length b length_b	100.680 Å
Unit-cell length c length_c	83.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	29.380 Å
R factor r_factor	0.2260
R_work r_work	0.2250
R_free r_free	0.2470

fit	/app/data/saxs_computation/zb/5zbq/5zbq.fit
pddf	/app/data/pr_computation/zb/5zbq/5zbq.pr.out
profile	/app/data/saxs_computation/zb/5zbq/5zbq.dat

The Crystal Structure of human neuropeptide Y Y1 receptor with UR-MK299

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

Neuropeptide Y receptor type 1,T4 Lysozyme

State in the Current Structure

Other States of the Same Protein in the Database

Neuropeptide Y receptor type 1,T4 Lysozyme

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)