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4hbm

Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase Mdm2

Homo sapiens

UniProt Q00987

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
10 Protein homooligomer Homooligomer Protein 2 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 water × 2 Consistent with protein count
11 Protein homooligomer Homooligomer Protein 2 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 water × 2 Consistent with protein count
12 Protein homooligomer Homooligomer Protein 2 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 water × 2 Consistent with protein count
2 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
7 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
8 Protein monomer Monomer Protein 1 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 water × 1 Consistent with protein count
9 Protein homooligomer Homooligomer Protein 2 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1z1m 2c6a 2c6b 2lzg 2ruh 3jzk 3lbk 3lbl 3lbl 3lbl 3tj2 3tj2

136 assemblies; showing the first 12

Homodimer
1t4e 2hdp 3lbk 3vbg 3vbg 4hbm 4hbm 4hbm 4hbm 4hg7 5hmh 5hmi

26 assemblies; showing the first 12

Homotetramer

None

Other homooligomers
1rv1

1 assemblies

Heteromeric or nucleic-acid complex
1t4f 1ycr 2f1y 2gv2 2m86 2mps 2vje 2vje 2vjf 2vjf 3eqs 3eqs

116 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name MDM2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–120； UniProt 6–125 Author chain B； PDBConstruct 1–120； UniProt 6–125 Author chain C； PDBConstruct 1–120； UniProt 6–125 Author chain D； PDBConstruct 1–120； UniProt 6–125 Author chain E； PDBConstruct 1–120； UniProt 6–125 Author chain F； PDBConstruct 1–120； UniProt 6–125 Author chain G； PDBConstruct 1–120； UniProt 6–125 Author chain H； PDBConstruct 1–120； UniProt 6–125

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_id4hbm
Deposition date deposition_date2012-09-28
Structure title titleOrdering of the N Terminus of Human MDM2 by Small Molecule Inhibitors
Keywords keywordsMDM2, p53, protein protein interaction, inhibitor, ligase-ligase inhibitor complex; ligase/ligase inhibitor
Experimental Method methodX-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.

4hbm__assembly_10__model_1

Assembly 10 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4hbm__assembly_10__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4hbm__assembly_10__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）17.98 Å
Rg (electron density)17.04 Å
Total Rg18.16 Å
Atom count1696
Residues205
Excluded volume30731 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4hbm__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4hbm__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4hbm__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 4hbm__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 4hbm__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 4hbm__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 4hbm__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 4hbm__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 4hbm__assembly_9__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 4hbm__assembly_10__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
11 1 4hbm__assembly_11__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
12 1 4hbm__assembly_12__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)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4hbma_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain
Domain ID domain_idd4hbmb_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain
Domain ID domain_idd4hbmc_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain
Domain ID domain_idd4hbmd_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain
Domain ID domain_idd4hbme_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain
Domain ID domain_idd4hbmf_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain
Domain ID domain_idd4hbmg_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain
Domain ID domain_idd4hbmh_
Class classa — All alpha proteins
Fold Fold folda.42 — SWIB/MDM2 domain
Superfamily Superfamily superfamilya.42.1 — SWIB/MDM2 domain
Family Family familya.42.1.1 — SWIB/MDM2 domain

CATH v4.4 (8 domains)

Domain ID domain_id4hbmA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
Domain ID domain_id4hbmB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
Domain ID domain_id4hbmC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
Domain ID domain_id4hbmD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
Domain ID domain_id4hbmE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
Domain ID domain_id4hbmF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
Domain ID domain_id4hbmG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
Domain ID domain_id4hbmH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology245 — MDM2
Homologous superfamily homologous superfamily10 — SWIB/MDM2 domain
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7. Citations (1)