SAXSdb — 7k89

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

Retinoid isomerohydrolase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (II) ION × 2 PALMITIC ACID × 2 TETRAETHYLENE GLYCOL × 2 SODIUM ION × 2 (1R)-3-amino-1-[3-(cyclohexylmethoxy)-4-fluorophenyl]propan-1-ol × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPE65_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–533； UniProt 2–533 Author chain B； PDBConstruct 2–533； UniProt 2–533

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	7k89
Deposition date deposition_date	2020-09-26
Structure title title	Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate
Keywords keywords	Non-heme iron, isomerohydrolase, inhibitor, beta-propeller, ISOMERASE, HYDROLASE-INHIBITOR complex; ISOMERASE,HYDROLASE/INHIBITOR
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.

7k89__assembly_1__model_1

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

Download this curve (.dat)

7k89__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7k89__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.46 Å
Rg (electron density)	31.78 Å
Total Rg	32.47 Å
Atom count	8250
Residues	1009
Excluded volume	147840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7k89__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 (7)

Entity 1 Entity 1 polymer

Description description	Retinoid isomerohydrolase
Molecular weight formula_weight	60935.0 kDa
EC 编号 ec_number	3.1.1.64,5.3.3.22
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9204

XSSQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	(1R)-3-amino-1-[3-(cyclohexylmethoxy)-4-fluorophenyl]propan-1-ol
Molecular weight formula_weight	281.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	800

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d7k89a_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.15 — Retinal pigment epithelial membrane protein-like
Family Family family	b.69.15.1 — RPE65-like

Domain ID domain_id	d7k89b_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.15 — Retinal pigment epithelial membrane protein-like
Family Family family	b.69.15.1 — RPE65-like

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Unit-cell length a length_a	175.695 Å
Unit-cell length b length_b	175.695 Å
Unit-cell length c length_c	86.214 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	47.840 Å
R factor r_factor	0.1904
R_work r_work	0.1889
R_free r_free	0.2172

Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate

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

Retinoid isomerohydrolase

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

7k89__assembly_1__model_1

7k89__assembly_1__model_1 | I(q)

7k89__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate

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

Retinoid isomerohydrolase

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

7k89__assembly_1__model_1

7k89__assembly_1__model_1 | I(q)

7k89__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)