SAXSdb — 9ipm

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

Gap junction delta-2 protein,Soluble cytochrome b562

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 6	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 12 TETRADECANE × 6	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 109–214； UniProt 23–128 Author chain B； PDBConstruct 109–214； UniProt 23–128 Author chain C； PDBConstruct 109–214； UniProt 23–128 Author chain D； PDBConstruct 109–214； UniProt 23–128 Author chain E； PDBConstruct 109–214； UniProt 23–128 Author chain F； PDBConstruct 109–214； UniProt 23–128

Gap junction delta-2 protein,Soluble cytochrome b562

Homo sapiens

UniProt Q9UKL4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 6	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 12 TETRADECANE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CXD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 1–108 Author chain A； PDBConstruct 215–348； UniProt 188–321 Author chain B； PDBConstruct 1–108； UniProt 1–108 Author chain B； PDBConstruct 215–348； UniProt 188–321 Author chain C； PDBConstruct 1–108； UniProt 1–108 Author chain C； PDBConstruct 215–348； UniProt 188–321 Author chain D； PDBConstruct 1–108； UniProt 1–108 Author chain D； PDBConstruct 215–348； UniProt 188–321 Author chain E； PDBConstruct 1–108； UniProt 1–108 Author chain E； PDBConstruct 215–348； UniProt 188–321 Author chain F； PDBConstruct 1–108； UniProt 1–108 Author chain F； PDBConstruct 215–348； UniProt 188–321

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	9ipm
Deposition date deposition_date	2024-07-11
Structure title title	Hemichannel sub-structure of Cx36/GJD2 gap junction intercellular channel (FN conformation) in soybean polar lipid nanodiscs, treated with a 20-fold molar excess of carbenoxolone
Keywords keywords	Gap junction, Connexin36, Inhibitor, Carbenoxolone, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

9ipm__assembly_1__model_1

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

Download this curve (.dat)

9ipm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ipm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.32 Å
Rg (electron density)	32.16 Å
Total Rg	33.07 Å
Atom count	8760
Residues	1026
Excluded volume	161400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ipm__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	Gap junction delta-2 protein,Soluble cytochrome b562
Molecular weight formula_weight	41035.4 kDa
Mutation mutation	M29W,H124I,R128L
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A,B,F,C,D
Atom count atom_count	8760

MGEWTILERLLEAAVQQHSTMIGRILLTVVVIFRILIVAIVGETVYDDEQTMFVCNTLQPGCNQACYDRAFPISHIRYWVFQIIMVCTPSLCFITYSVHQSAKQRERRADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLKLRRQEGISRFYIIQVVFRNALEIGFLVGQYFLYGFSVPGLYECNRYPCIKEVECYVSRPTEKTVFLVFMFAVSGICVVLNLAELNHLGWRKIKLAVRGAQAKRKSIYEIRNKDLPRVSVPNFGRTQSSDSAYVSRGDMLEVLFQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	677.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	TETRADECANE
Molecular weight formula_weight	198.4 kDa
Source method src_method	syn
Copy count entity_count	6

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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	—

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

Resolution resolution	3.56 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	111066

Hemichannel sub-structure of Cx36/GJD2 gap junction intercellular channel (FN conformation) in soybean polar lipid nanodiscs, treated with a 20-fold molar excess of carbenoxolone

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

Gap junction delta-2 protein,Soluble cytochrome b562

State in the Current Structure

Other States of the Same Protein in the Database

Gap junction delta-2 protein,Soluble cytochrome b562

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

9ipm__assembly_1__model_1

9ipm__assembly_1__model_1 | I(q)

9ipm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)

Hemichannel sub-structure of Cx36/GJD2 gap junction intercellular channel (FN conformation) in soybean polar lipid nanodiscs, treated with a 20-fold molar excess of carbenoxolone

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

Gap junction delta-2 protein,Soluble cytochrome b562

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Gap junction delta-2 protein,Soluble cytochrome b562

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

9ipm__assembly_1__model_1

9ipm__assembly_1__model_1 | I(q)

9ipm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)