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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide × 1	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide × 1	Consistent with protein count

Other States of the Same Protein in the Database

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. 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.

5zbq__assembly_1__model_1

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

Download this curve (.dat)

5zbq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zbq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.38 Å
Rg (electron density)	30.66 Å
Total Rg	31.13 Å
Atom count	3760
Residues	463
Excluded volume	68111 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zbq__assembly_1__model_1`	monomeric （1）	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 (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

Source Source

Source organism organism	Enterobacteria phage RB55
NCBI taxonomy ID ncbi_taxonomy_id	697289
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5zbq__assembly_1__model_1

5zbq__assembly_1__model_1 | I(q)

5zbq__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Neuropeptide Y receptor type 1,T4 Lysozyme

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

5zbq__assembly_1__model_1

5zbq__assembly_1__model_1 | I(q)

5zbq__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)