SAXSdb — 4yos

▼

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

Retinoblastoma-like protein 1,Retinoblastoma-like protein 1

Myotis davidii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Protein lin-52 homolog × 1 （Q5ZJQ3） SULFATE ION × 2 1,2-ETHANEDIOL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	L5LUA8_MYODS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 214–369； UniProt 1659–1835

Retinoblastoma-like protein 1,Retinoblastoma-like protein 1

Myotis davidii

UniProt P28749

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Protein lin-52 homolog × 1 （Q5ZJQ3） SULFATE ION × 2 1,2-ETHANEDIOL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–213； UniProt 391–600

Protein lin-52 homolog

OrganismNot specified

UniProt Q5ZJQ3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Retinoblastoma-like protein 1,Retinoblastoma-like protein 1 × 1 （L5LUA8,P28749） SULFATE ION × 2 1,2-ETHANEDIOL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LIN52_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–20； UniProt 11–30

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	4yos
Deposition date deposition_date	2015-03-12
Structure title title	p107 pocket domain complexed with LIN52 peptide
Keywords keywords	Cyclin Box Pocket Transcriptional Regulator DREAM, TRANSCRIPTION; TRANSCRIPTION
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.

4yos__assembly_1__model_1

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

Download this curve (.dat)

4yos__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yos__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.88 Å
Rg (electron density)	22.84 Å
Total Rg	23.76 Å
Atom count	2875
Residues	352
Excluded volume	51554 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yos__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
Molecular weight formula_weight	43037.8 kDa
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	2970

GEFTQSVSRLQSIVAGLKNAPSDQLINIFESCVRNPVENIMKILKGIGETFCQHYTQSTDEQPGSHIDFAVNRLKLAEILYYKILETVMVQETRRLHGMDMSVLLEQDIFHRSLMACCLEIVLFAYSSPRTFPWIIEVLNLQPFYFYKVIEVVIRSEEGLSRDMVKHLNSIEEQILESLAWSHDSALWEALQVSANKVPTCEEVIFPNNFETGRPKRTGSLALFYRKVYHLASVRLRDLCLKLDVSNELRRKIWTCFEFTLVHCPDLMKDRHLDQLLLCAFYIMAKVTKEERTFQEIMKSYRNQPQANSHVYRSVLLKSIKEERGDLIKFYNTIYVGRVKSFALKYDLANQDHMMDAPPLSPFPHIKQQ

Source Source

Source organism organism	Myotis davidii
Common name common_name	;David's myotis ;
NCBI taxonomy ID ncbi_taxonomy_id	225400
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein lin-52 homolog
Molecular weight formula_weight	2385.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

EASLLSFEKLDRASPDLWPE

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4yosA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4yosA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

▶

Unit-cell length a length_a	75.430 Å
Unit-cell length b length_b	101.060 Å
Unit-cell length c length_c	140.685 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	60.449 Å
R factor r_factor	0.2033
R_work r_work	0.1989
R_free r_free	0.2424

p107 pocket domain complexed with LIN52 peptide

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

Retinoblastoma-like protein 1,Retinoblastoma-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Retinoblastoma-like protein 1,Retinoblastoma-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Protein lin-52 homolog

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

4yos__assembly_1__model_1

4yos__assembly_1__model_1 | I(q)

4yos__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

p107 pocket domain complexed with LIN52 peptide

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

Retinoblastoma-like protein 1,Retinoblastoma-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Retinoblastoma-like protein 1,Retinoblastoma-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein lin-52 homolog

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

4yos__assembly_1__model_1

4yos__assembly_1__model_1 | I(q)

4yos__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)