SAXSdb — 6v55

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

Adhesion G-protein coupled receptor G6

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGRG6_DANRE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–780； UniProt 37–839 Author chain Q； PDBConstruct 1–12； UniProt 828–839

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	6v55
Deposition date deposition_date	2019-12-03
Structure title title	Full extracellular region of zebrafish Gpr126/Adgrg6
Keywords keywords	adhesion G-protein coupled receptor, myelination, calcium-binding, CELL ADHESION; CELL ADHESION
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.

6v55__assembly_1__model_1

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

Download this curve (.dat)

6v55__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6v55__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.53 Å
Rg (electron density)	41.97 Å
Total Rg	41.88 Å
Atom count	5917
Residues	753
Excluded volume	104970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6v55__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Adhesion G-protein coupled receptor G6
Molecular weight formula_weight	86436.7 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	6114

ASTSCNVVLTDSQGSFTSPCYPNDYPPSQSCNWTIQAPAGFIVQITFLDFELEEAQGCIYDRVVVKTGTSDAKFCGLTANGLTLNSTGNVMEVFFNSDFSVQKKGFHISYKQVAVTLRNQKVTMPKSSKTILRVSNSISIPVLTAFTVCFEIARTAQKATETIFTLSDAAGTSILAFEKTSNGMELFIGASYCSVDNFLTSSDITATMKPLCLTWTKSSGLIGVYFEGHYFSSICSASQIYTLQSGGLLQIAGKGSSSVSVDDQNLDGFIYNFRLWDHAMLSSELSALTCDTVGNVVDWDHSYWTIPGSSTQTDSTLSCSTAITTLSPGTAGCASGLGCPEDIFYRSTLVVTDEQTPDRDATAIISQWLNQTFQNWMYRVYVDGISLQLITVLSRITTTRQIYLALLVYKNTTDVNLAEVEIESMLRSAPAIGNGLTLDSVTVNLMENCQADEFPVHYRWPESRPTVTQYVPCFPYKDRNASRTCMINRDNYTSFWALPDRGNCTNITSITVSQENAMDVAVQLADISNNGLSKEELTQVVTKVMELVNIAKINATLASTVVTIISNVMVSSEDAQKDASETALKAVDELVQKIEFDGPSLTISSKNLVVGVSALDTTNFNGSTLSAFIATNTTDPQIDFDSEAHNALAVVTLPPTLLQNLSLSQIEKVSRINFMFFGRTGLFQDHQNNGLTLNSYVVASSVGNFTIKNLQDPVRIEIAHLEYQKDPNPQCVFWDFNLQNYSGGWNSDGCKVGSDSNSNRTVCLCNHLTHFGILMDVSRAHHHHHHHH

Source Source

Source organism organism	Danio rerio
Common name common_name	Zebrafish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Adhesion G-protein coupled receptor G6
Molecular weight formula_weight	1348.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

THFGILMDVSRA

Source Source

Source organism organism	Danio rerio
Common name common_name	Zebrafish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	11

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	197

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6v55A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	290 — Spermadhesin, CUB domain

Domain ID domain_id	6v55A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	6v55A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	144.960 Å
Unit-cell length b length_b	59.448 Å
Unit-cell length c length_c	168.385 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.82 °
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	monoclinic

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	47.900 Å
R factor r_factor	0.2152
R_work r_work	0.2121
R_free r_free	0.2717

Full extracellular region of zebrafish Gpr126/Adgrg6

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

Adhesion G-protein coupled receptor G6

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

6v55__assembly_1__model_1

6v55__assembly_1__model_1 | I(q)

6v55__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Full extracellular region of zebrafish Gpr126/Adgrg6

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

Adhesion G-protein coupled receptor G6

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

6v55__assembly_1__model_1

6v55__assembly_1__model_1 | I(q)

6v55__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)