SAXSdb — 6br3

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

Nuclear receptor ROR-gamma

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(4S)-2-METHYL-2,4-PENTANEDIOL × 1 ;{cis-3-[(5R)-5-[(7-fluoro-1,1-dimethyl-1H-inden-5-yl)carbamoyl]-2-methoxy-7,8-dihydro-1,6-naphthyridine-6(5H)-carbonyl]cyclobutyl}acetic acid ; × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	(4S)-2-METHYL-2,4-PENTANEDIOL × 2 ;{cis-3-[(5R)-5-[(7-fluoro-1,1-dimethyl-1H-inden-5-yl)carbamoyl]-2-methoxy-7,8-dihydro-1,6-naphthyridine-6(5H)-carbonyl]cyclobutyl}acetic acid ; × 2 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(4S)-2-METHYL-2,4-PENTANEDIOL × 1 ;{cis-3-[(5R)-5-[(7-fluoro-1,1-dimethyl-1H-inden-5-yl)carbamoyl]-2-methoxy-7,8-dihydro-1,6-naphthyridine-6(5H)-carbonyl]cyclobutyl}acetic acid ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RORG_HUMAN
Isoform	P51449-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 244–459 Author chain B； PDBConstruct 1–216； UniProt 244–459

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	6br3
Deposition date deposition_date	2017-11-29
Structure title title	Structure of RORgt in complex with a novel inverse agonist TAK-828.
Keywords keywords	Nuclear Hormone Receptor, inverse agonist, complex, transcription-agonist complex; transcription/agonist
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.

6br3__assembly_1__model_1

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

Download this curve (.dat)

6br3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6br3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.58 Å
Rg (electron density)	18.33 Å
Total Rg	19.34 Å
Atom count	1802
Residues	216
Excluded volume	32165 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6br3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6br3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6br3__assembly_3__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	Nuclear receptor ROR-gamma
Molecular weight formula_weight	25100.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3582

ASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHV

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	;{cis-3-[(5R)-5-[(7-fluoro-1,1-dimethyl-1H-inden-5-yl)carbamoyl]-2-methoxy-7,8-dihydro-1,6-naphthyridine-6(5H)-carbonyl]cyclobutyl}acetic acid ;
Molecular weight formula_weight	507.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6br3a_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.0 — automated matches

Domain ID domain_id	d6br3b_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6br3A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	6br3B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

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Unit-cell length a length_a	99.537 Å
Unit-cell length b length_b	99.537 Å
Unit-cell length c length_c	127.524 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1979
R_work r_work	0.1957
R_free r_free	0.2387

Structure of RORgt in complex with a novel inverse agonist TAK-828.

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

Nuclear receptor ROR-gamma

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

6br3__assembly_1__model_1

6br3__assembly_1__model_1 | I(q)

6br3__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of RORgt in complex with a novel inverse agonist TAK-828.

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

Nuclear receptor ROR-gamma

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

6br3__assembly_1__model_1

6br3__assembly_1__model_1 | I(q)

6br3__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)