SAXSdb — 4jrg

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

E3 ubiquitin-protein ligase Mdm2

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(3R,4R,5S)-3-(3-chlorophenyl)-4-(4-chlorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(3R,4R,5S)-3-(3-chlorophenyl)-4-(4-chlorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDM2_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 21–105 Author chain B； PDBConstruct 1–85； UniProt 21–105

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	4jrg
Deposition date deposition_date	2013-03-21
Structure title title	The 1.9A crystal structure of humanized Xenopus MDM2 with RO5313109 - a pyrrolidine MDM2 inhibitor
Keywords keywords	protein-inhibitor complex, pyrrolidine, E3 ubiquitin ligase, P53, nucleus, LIGASE-LIGASE INHIBITOR complex; LIGASE/LIGASE 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.

4jrg__assembly_1__model_1

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

Download this curve (.dat)

4jrg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jrg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.03 Å
Rg (electron density)	12.53 Å
Total Rg	13.97 Å
Atom count	718
Residues	84
Excluded volume	13023 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jrg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4jrg__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase Mdm2
Molecular weight formula_weight	9831.4 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	I50L, P92H, L95I
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	1584

EKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLVS

Source Source

Source organism organism	Xenopus laevis
Common name common_name	clawed frog,common platanna,platanna
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(3R,4R,5S)-3-(3-chlorophenyl)-4-(4-chlorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide
Molecular weight formula_weight	518.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4jrga_
Class class	a — All alpha proteins
Fold Fold fold	a.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamily	a.42.1 — SWIB/MDM2 domain
Family Family family	a.42.1.1 — SWIB/MDM2 domain

Domain ID domain_id	d4jrgb_
Class class	a — All alpha proteins
Fold Fold fold	a.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamily	a.42.1 — SWIB/MDM2 domain
Family Family family	a.42.1.1 — SWIB/MDM2 domain

CATH v4.4 (2 domains)

Domain ID domain_id	4jrgA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	245 — MDM2
Homologous superfamily homologous superfamily	10 — SWIB/MDM2 domain

Domain ID domain_id	4jrgB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	245 — MDM2
Homologous superfamily homologous superfamily	10 — SWIB/MDM2 domain

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Unit-cell length a length_a	73.542 Å
Unit-cell length b length_b	72.796 Å
Unit-cell length c length_c	43.865 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	28.030 Å
R factor r_factor	0.2520
R_work r_work	0.2500
R_free r_free	0.2880

The 1.9A crystal structure of humanized Xenopus MDM2 with RO5313109 - a pyrrolidine MDM2 inhibitor

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

E3 ubiquitin-protein ligase Mdm2

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

4jrg__assembly_1__model_1

4jrg__assembly_1__model_1 | I(q)

4jrg__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

The 1.9A crystal structure of humanized Xenopus MDM2 with RO5313109 - a pyrrolidine MDM2 inhibitor

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

E3 ubiquitin-protein ligase Mdm2

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

4jrg__assembly_1__model_1

4jrg__assembly_1__model_1 | I(q)

4jrg__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)