6sqr

Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub

Method: X-RAY DIFFRACTION

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

E3 ubiquitin-protein ligase Mdm2

Felis catus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Ubiquitin-conjugating enzyme E2 D2 × 4 （P62837） Ubiquitin-40S ribosomal protein S27a × 3 （J3QTR3） Polyubiquitin-C × 1 （P0CG48） 1,2-ETHANEDIOL × 12 ZINC ION × 8 NITRATE ION × 3 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDM2_FELCA
Isoform	—
PDB entities	1, 4, 5
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 423–491 Author chain D； PDBConstruct 1–64； UniProt 428–491 Author chain J； PDBConstruct 1–64； UniProt 428–491 Author chain G； PDBConstruct 1–63； UniProt 429–491

Ubiquitin-conjugating enzyme E2 D2

Homo sapiens

UniProt P62837

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	E3 ubiquitin-protein ligase Mdm2 × 1 （Q7YRZ8） Ubiquitin-40S ribosomal protein S27a × 3 （J3QTR3） E3 ubiquitin-protein ligase Mdm2 × 2 （Q7YRZ8） E3 ubiquitin-protein ligase Mdm2 × 1 （Q7YRZ8） Polyubiquitin-C × 1 （P0CG48） 1,2-ETHANEDIOL × 12 ZINC ION × 8 NITRATE ION × 3 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UB2D2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–146； UniProt 2–147 Author chain E； PDBConstruct 1–146； UniProt 2–147 Author chain H； PDBConstruct 1–146； UniProt 2–147 Author chain K； PDBConstruct 1–146； UniProt 2–147

Ubiquitin-40S ribosomal protein S27a

Homo sapiens

UniProt J3QTR3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	E3 ubiquitin-protein ligase Mdm2 × 1 （Q7YRZ8） Ubiquitin-conjugating enzyme E2 D2 × 4 （P62837） E3 ubiquitin-protein ligase Mdm2 × 2 （Q7YRZ8） E3 ubiquitin-protein ligase Mdm2 × 1 （Q7YRZ8） Polyubiquitin-C × 1 （P0CG48） 1,2-ETHANEDIOL × 12 ZINC ION × 8 NITRATE ION × 3 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	J3QTR3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–77； UniProt 1–76 Author chain F； PDBConstruct 2–77； UniProt 1–76 Author chain L； PDBConstruct 2–77； UniProt 1–76

Polyubiquitin-C

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	E3 ubiquitin-protein ligase Mdm2 × 1 （Q7YRZ8） Ubiquitin-conjugating enzyme E2 D2 × 4 （P62837） Ubiquitin-40S ribosomal protein S27a × 3 （J3QTR3） E3 ubiquitin-protein ligase Mdm2 × 2 （Q7YRZ8） E3 ubiquitin-protein ligase Mdm2 × 1 （Q7YRZ8） 1,2-ETHANEDIOL × 12 ZINC ION × 8 NITRATE ION × 3 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain I； PDBConstruct 1–76； UniProt 1–76

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	6sqr
Deposition date deposition_date	2019-09-04
Structure title title	Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub
Keywords keywords	MDM2, MDMX, p53, E3, E2, ubiquitin, ubiquitin ligase, phosphorylation, 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.

6sqr__assembly_1__model_1

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

Download this curve (.dat)

6sqr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6sqr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.63 Å
Rg (electron density)	39.18 Å
Total Rg	39.15 Å
Atom count	9129
Residues	1151
Excluded volume	164000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6sqr__assembly_1__model_1`	dodecameric （12）	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 (10)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase Mdm2
Molecular weight formula_weight	7849.4 kDa
EC 编号 ec_number	2.3.2.27
Mutation mutation	S429E, G443T
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	9560

EEIVEPEFPHNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP

Source Source

Source organism organism	Felis catus
Common name common_name	Cat
NCBI taxonomy ID ncbi_taxonomy_id	9685
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin-conjugating enzyme E2 D2
Molecular weight formula_weight	16720.2 kDa
EC 编号 ec_number	2.3.2.23,2.3.2.24
Mutation mutation	S22R, C85K
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

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 3 Entity 3 polymer

Description description	Ubiquitin-40S ribosomal protein S27a
Molecular weight formula_weight	8663.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,L

SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 4 Entity 4 polymer

Description description	E3 ubiquitin-protein ligase Mdm2
Molecular weight formula_weight	7249.8 kDa
EC 编号 ec_number	2.3.2.27
Mutation mutation	S429E, G443T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,J

PEFPHNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP

Source Source

Source organism organism	Felis catus
Common name common_name	Cat
NCBI taxonomy ID ncbi_taxonomy_id	9685
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	E3 ubiquitin-protein ligase Mdm2
Molecular weight formula_weight	7152.7 kDa
EC 编号 ec_number	2.3.2.27
Mutation mutation	S429E, G443T
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

EFPHNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP

Source Source

Source organism organism	Felis catus
Common name common_name	Cat
NCBI taxonomy ID ncbi_taxonomy_id	9685
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Polyubiquitin-C
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 9 Entity 9 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	420

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6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d6sqrb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d6sqrc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6sqrc2
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	d6sqre_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d6sqrf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6sqrf2
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	d6sqrh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d6sqri_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6sqrk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d6sqrl1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6sqrl2
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 (8 domains)

Domain ID domain_id	6sqrA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6sqrC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6sqrD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6sqrF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6sqrG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6sqrI01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6sqrJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6sqrL01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	56.510 Å
Unit-cell length b length_b	163.880 Å
Unit-cell length c length_c	70.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	70.000 Å
R factor r_factor	—
R_work r_work	0.1660
R_free r_free	0.2270

Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub

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

Ubiquitin-conjugating enzyme E2 D2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-40S ribosomal protein S27a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin-C

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

6sqr__assembly_1__model_1

6sqr__assembly_1__model_1 | I(q)

6sqr__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. Citations (1)