SAXSdb — 1t4e

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

Ubiquitin-protein ligase E3 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	(4-CHLOROPHENYL)[3-(4-CHLOROPHENYL)-7-IODO-2,5-DIOXO-1,2,3,5-TETRAHYDRO-4H-1,4-BENZODIAZEPIN-4-YL]ACETIC ACID × 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 2–96； UniProt 17–111 Author chain B； PDBConstruct 2–96； UniProt 17–111

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	1t4e
Deposition date deposition_date	2004-04-29
Structure title title	Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor
Keywords keywords	MDM2-Inhibitor complex, LIGASE; LIGASE
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.

1t4e__assembly_1__model_1

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

Download this curve (.dat)

1t4e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t4e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.58 Å
Rg (electron density)	18.85 Å
Total Rg	19.62 Å
Atom count	1632
Residues	192
Excluded volume	29676 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t4e__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 (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-protein ligase E3 Mdm2
Molecular weight formula_weight	11156.1 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	17-111, additional GLY at N-terminus
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	1682

GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN

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 BL21

Entity 2 Entity 2 non-polymer

Description description	(4-CHLOROPHENYL)[3-(4-CHLOROPHENYL)-7-IODO-2,5-DIOXO-1,2,3,5-TETRAHYDRO-4H-1,4-BENZODIAZEPIN-4-YL]ACETIC ACID
Molecular weight formula_weight	581.2 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	50

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1t4ea2
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	d1t4ea3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1t4eb2
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	d1t4eb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1t4eA00
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	1t4eB00
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	98.486 Å
Unit-cell length b length_b	98.486 Å
Unit-cell length c length_c	74.038 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 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	55.910 Å
R factor r_factor	—
R_work r_work	0.2390
R_free r_free	0.2760

Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor

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

Ubiquitin-protein ligase E3 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

1t4e__assembly_1__model_1

1t4e__assembly_1__model_1 | I(q)

1t4e__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor

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

Ubiquitin-protein ligase E3 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

1t4e__assembly_1__model_1

1t4e__assembly_1__model_1 | I(q)

1t4e__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)