SAXSdb — 5dgy

▼

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

Endolysin,Rhodopsin,S-arrestin

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENLYS_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–160； UniProt 2–161 Author chain B； PDBConstruct 1–160； UniProt 2–161 Author chain C； PDBConstruct 1–160； UniProt 2–161 Author chain D； PDBConstruct 1–160； UniProt 2–161

Endolysin,Rhodopsin,S-arrestin

Mus musculus

UniProt P08100

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OPSD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 161–508； UniProt 1–348 Author chain B； PDBConstruct 161–508； UniProt 1–348 Author chain C； PDBConstruct 161–508； UniProt 1–348 Author chain D； PDBConstruct 161–508； UniProt 1–348

Endolysin,Rhodopsin,S-arrestin

Mus musculus

UniProt P20443

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARRS_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 524–906； UniProt 10–392 Author chain B； PDBConstruct 524–906； UniProt 10–392 Author chain C； PDBConstruct 524–906； UniProt 10–392 Author chain D； PDBConstruct 524–906； UniProt 10–392

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5dgy
Deposition date deposition_date	2015-08-28
Structure title title	Crystal structure of rhodopsin bound to visual arrestin
Keywords keywords	GPCR, rhodopsin, arrestin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5dgy__assembly_1__model_1

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

Download this curve (.dat)

5dgy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dgy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	62.99 Å
Rg (electron density)	64.47 Å
Total Rg	63.93 Å
Atom count	12796
Residues	1622
Excluded volume	231400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dgy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5dgy__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Description description	Endolysin,Rhodopsin,S-arrestin
Molecular weight formula_weight	100861.1 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	24665

NIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYMCGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLQGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIYVIAFLICWVPYASVAFYIFTHQGSCFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPAAAAGSAGSAGSAGSASHVIFKKVSRDKSVTIYLGKRDYVDHVSQVEPVDGVVLVDPELVKGKKVYVTLTCAFRYGQEDIDVMGLTFRRDLYFSRVQVYPPVGAMSVLTQLQESLLKKLGDNTYPFLLTFPDYLPCSVMLQPAPQDVGKSCGVDFEVKAFASDITDPEEDKIPKKSSVRLLIRKVQHAPPEMGPQPSAEASWQFFMSDKPLNLSVSLSKEIYFHGEPIPVTVTVTNNTDKVVKKIKVSVEQIANVVLYSSDYYVKPVASEETQEKVQPNSTLTKTLVLVPLLANNRERRGIALDGKIKHEDTNLASSTIIKEGIDRTVMGILVSYHIKVKLTVSGFLGELTSSEVATEVPFRLMHPQPEDPAKESVQDENAAAEEFARQNLKDTGENTE

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

▶

Unit-cell length a length_a	107.484 Å
Unit-cell length b length_b	107.258 Å
Unit-cell length c length_c	460.314 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	7.700 Å
Low-resolution limit resolution_low	29.978 Å
R factor r_factor	0.2877
R_work r_work	0.2853
R_free r_free	0.3351

Crystal structure of rhodopsin bound to visual arrestin

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

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Endolysin,Rhodopsin,S-arrestin

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

5dgy__assembly_1__model_1

5dgy__assembly_1__model_1 | I(q)

5dgy__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of rhodopsin bound to visual arrestin

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

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Endolysin,Rhodopsin,S-arrestin

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

5dgy__assembly_1__model_1

5dgy__assembly_1__model_1 | I(q)

5dgy__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)