SAXSdb — 6q9s

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

Protein Mdm4

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;3-[[6-chloranyl-3-[3-[(1~{S})-1-(2,4-dichlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]carbonylamino]-4-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]benzoic acid ; × 1 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 4 SULFATE ION × 1 SODIUM ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;3-[[6-chloranyl-3-[3-[(1~{S})-1-(2,4-dichlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]carbonylamino]-4-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]benzoic acid ; × 1 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 7 SULFATE ION × 2 SODIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;3-[[6-chloranyl-3-[3-[(1~{S})-1-(2,4-dichlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]carbonylamino]-4-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]benzoic acid ; × 1 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 2 SULFATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDM4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–100； UniProt 14–111 Author chain B； PDBConstruct 3–100； UniProt 14–111 Author chain C； PDBConstruct 3–100； UniProt 14–111

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	6q9s
Deposition date deposition_date	2018-12-18
Structure title title	HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
Keywords keywords	HDMX, MDM4, APOPTOSIS; APOPTOSIS
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.

6q9s__assembly_1__model_1

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

Download this curve (.dat)

6q9s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6q9s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.66 Å
Rg (electron density)	13.07 Å
Total Rg	14.52 Å
Atom count	829
Residues	87
Excluded volume	15191 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6q9s__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6q9s__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6q9s__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	Protein Mdm4
Molecular weight formula_weight	11187.0 kDa
Mutation mutation	C17S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B
Atom count atom_count	2547

GPDSASRISPGQINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLAT

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	;3-[[6-chloranyl-3-[3-[(1~{S})-1-(2,4-dichlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]carbonylamino]-4-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]benzoic acid ;
Molecular weight formula_weight	812.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE
Molecular weight formula_weight	264.3 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6q9sa_
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.42.1.0 — automated matches

Domain ID domain_id	d6q9sb_
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.42.1.0 — automated matches

Domain ID domain_id	d6q9sc_
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.42.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	6q9sA00
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	6q9sB00
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	6q9sC00
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	93.581 Å
Unit-cell length b length_b	93.581 Å
Unit-cell length c length_c	198.467 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	36

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.2500
R_work r_work	0.2491
R_free r_free	0.2682

HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes

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

Protein Mdm4

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

6q9s__assembly_1__model_1

6q9s__assembly_1__model_1 | I(q)

6q9s__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes

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

Protein Mdm4

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

6q9s__assembly_1__model_1

6q9s__assembly_1__model_1 | I(q)

6q9s__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)