SAXSdb — 3vbg

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

E3 ubiquitin-protein ligase Mdm2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	(5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDM2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 25–109 Author chain B； PDBConstruct 1–85； UniProt 25–109 Author chain C； PDBConstruct 1–85； UniProt 25–109 Author chain D； PDBConstruct 1–85； UniProt 25–109

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	3vbg
Deposition date deposition_date	2012-01-02
Structure title title	Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443
Keywords keywords	Ligase, MDM2, MDMX, P53, Ligase-ligase activator complex; Ligase/ligase activator
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.

3vbg__assembly_1__model_1

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

Download this curve (.dat)

3vbg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vbg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.10 Å
Rg (electron density)	17.35 Å
Total Rg	18.45 Å
Atom count	1461
Residues	169
Excluded volume	26478 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vbg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vbg__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase Mdm2
Molecular weight formula_weight	10060.8 kDa
EC 编号 ec_number	6.3.2.-
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	2941

ETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV

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	(5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione
Molecular weight formula_weight	401.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3vbga_
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	d3vbgb_
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	d3vbgc_
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	d3vbgd_
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 (4 domains)

Domain ID domain_id	3vbgA00
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	3vbgB00
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	3vbgC00
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	3vbgD00
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	64.392 Å
Unit-cell length b length_b	64.392 Å
Unit-cell length c length_c	167.587 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 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1842
R_work r_work	0.1822
R_free r_free	0.2199

Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443

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

3vbg__assembly_1__model_1

3vbg__assembly_1__model_1 | I(q)

3vbg__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443

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

3vbg__assembly_1__model_1

3vbg__assembly_1__model_1 | I(q)

3vbg__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)