SAXSdb — 6ko5

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

Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Fab7881 Heavy Chain × 1 Fab7881 Light Chain × 1 6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3,2-d]pyrimidin-4-one × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C562_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–106； UniProt 23–128

Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1

Homo sapiens

UniProt Q92847

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Fab7881 Heavy Chain × 1 Fab7881 Light Chain × 1 6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3,2-d]pyrimidin-4-one × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GHSR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 107–424； UniProt 29–346

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	6ko5
Deposition date deposition_date	2019-08-08
Structure title title	Complex structure of Ghrelin receptor with Fab
Keywords keywords	G-PROTEIN COUPLED RECEPTOR, GHRELIN, ANTAGONIST-BOUND COMPLEX, MEMBRANE PROTEIN; MEMBRANE 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.

6ko5__assembly_1__model_1

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

Download this curve (.dat)

6ko5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ko5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.82 Å
Rg (electron density)	51.04 Å
Total Rg	50.74 Å
Atom count	6543
Residues	835
Excluded volume	117330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ko5__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	Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1
Molecular weight formula_weight	47889.0 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	6543

ADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLSLGDELLQLFPAPLLAGVTATCVALFVVGIAGNLLTMLVVSRFRELRTTTNLYLSSMAFSDLLIFLCMPLDLVRLWQYRPWNFGDLLCKLFQFVSESCTYAKVLTITALSVERYFAICFPLRAKVVVTKGRVKLVIFVIWAVAFCSAGPIFVLVGVEHEQGTDPWDTNECRPTEFAVRSGLLTVMVWVSSIFFFLPVFCLTVLYSLIGRKLWRRRRGDAVVGASLRDQNHKQTVKMLAVVVFAFILCWLPFHVGRYLFSKSFEPGSLEIAQISQYCNLVSFVLFYLSAAINPILYNIMSKKYRVAVFRLLGFEPFSQR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Fab7881 Heavy Chain
Molecular weight formula_weight	23332.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLQQSGAELVRPGASVKLSCKASGYTFTDYEMHWVKQTPVHGLEWIGAIDPETGGTVYNQKFKGKATLTADISSTTAYMELRSLTSEDSAVYFCISEDIDESKDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Entity 3 Entity 3 polymer

Description description	Fab7881 Light Chain
Molecular weight formula_weight	24279.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVMTQSPSSLAVSAGEKVTLSCKSSQSLFNSRTRKNYLAWYQQKPGLSPTLLIYWASTRKSGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYYLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 4 Entity 4 non-polymer

Description description	6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3,2-d]pyrimidin-4-one
Molecular weight formula_weight	489.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6ko5A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	10 — Cytochrome c/b562

Domain ID domain_id	6ko5A02
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	6ko5H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6ko5H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6ko5L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6ko5L02
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	253.760 Å
Unit-cell length b length_b	44.750 Å
Unit-cell length c length_c	94.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	49.421 Å
R factor r_factor	0.2131
R_work r_work	0.2105
R_free r_free	0.2576

Complex structure of Ghrelin receptor with Fab

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

Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1

State in the Current Structure

Other States of the Same Protein in the Database

Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1

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

6ko5__assembly_1__model_1

6ko5__assembly_1__model_1 | I(q)

6ko5__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Complex structure of Ghrelin receptor with Fab

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

Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1

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

6ko5__assembly_1__model_1

6ko5__assembly_1__model_1 | I(q)

6ko5__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)