SAXSdb — 6aky

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

C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	ZINC ION × 1 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 ;4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-3-yl)propyl]cyclohexane-1-carboxamide ; × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUBR_CLOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 226–279； UniProt 1–54

C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5

Homo sapiens

UniProt P51681

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	ZINC ION × 1 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 ;4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-3-yl)propyl]cyclohexane-1-carboxamide ; × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCR5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–225； UniProt 2–223 Author chain A； PDBConstruct 280–372； UniProt 227–319

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	6aky
Deposition date deposition_date	2018-09-04
Structure title title	The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34
Keywords keywords	G Protein-Coupled Receptor Chemokine Receptor CCR5 Antagonist 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.

6aky__assembly_1__model_1

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

Download this curve (.dat)

6aky__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6aky__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.40 Å
Rg (electron density)	25.05 Å
Total Rg	25.87 Å
Atom count	2706
Residues	340
Excluded volume	49346 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6aky__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 (4)

Entity 1 Entity 1 polymer

Description description	C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
Molecular weight formula_weight	43876.2 kDa
Mutation mutation	C58Y, G163N, A233D, K303E
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	2706

GAPDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINYKRLKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFIILLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPNIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEEEKKRHRDVRLIFTIMIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFVGEEFRNYLLVFFQKHIAKRGRPLEVLFQ

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	;4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-3-yl)propyl]cyclohexane-1-carboxamide ;
Molecular weight formula_weight	519.7 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	35.585 Å
Unit-cell length b length_b	101.483 Å
Unit-cell length c length_c	136.569 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	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	31.560 Å
R factor r_factor	0.2750
R_work r_work	0.2750
R_free r_free	0.2830

The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34

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

C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5

State in the Current Structure

Other States of the Same Protein in the Database

C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5

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

6aky__assembly_1__model_1

6aky__assembly_1__model_1 | I(q)

6aky__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34

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

C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5

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

6aky__assembly_1__model_1

6aky__assembly_1__model_1 | I(q)

6aky__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)