SAXSdb — 5vkc

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

Induced myeloid leukemia cell differentiation protein Mcl-1

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	;7-(3-{[4-(4-acetylpiperazin-1-yl)phenoxy]methyl}-1,5-dimethyl-1H-pyrazol-4-yl)-3-{3-[(naphthalen-1-yl)oxy]propyl}-1-[(pyridin-3-yl)methyl]-1H-indole-2-carboxylic acid ; × 2 ZINC ION × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–157； UniProt 174–326 Author chain B； PDBConstruct 5–157； UniProt 174–326

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	5vkc
Deposition date deposition_date	2017-04-21
Structure title title	Crystal structure of MCL-1 in complex with a BIM competitive inhibitor
Keywords keywords	MCL-1, signaling protein-inhibitor complex; signaling protein/inhibitor
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.

5vkc__assembly_1__model_1

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

Download this curve (.dat)

5vkc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vkc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.45 Å
Rg (electron density)	24.47 Å
Total Rg	25.49 Å
Atom count	2448
Residues	288
Excluded volume	43762 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vkc__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 (4)

Entity 1 Entity 1 polymer

Description description	Induced myeloid leukemia cell differentiation protein Mcl-1
Molecular weight formula_weight	17882.4 kDa
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	2572

GSMDLYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHVEDLEG

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	;7-(3-{[4-(4-acetylpiperazin-1-yl)phenoxy]methyl}-1,5-dimethyl-1H-pyrazol-4-yl)-3-{3-[(naphthalen-1-yl)oxy]propyl}-1-[(pyridin-3-yl)methyl]-1H-indole-2-carboxylic acid ;
Molecular weight formula_weight	762.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5vkca1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.4 — Bcl-2 inhibitors of programmed cell death
Family Family family	f.1.4.1 — Bcl-2 inhibitors of programmed cell death

Domain ID domain_id	d5vkca2
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	d5vkcb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.4 — Bcl-2 inhibitors of programmed cell death
Family Family family	f.1.4.1 — Bcl-2 inhibitors of programmed cell death

Domain ID domain_id	d5vkcb2
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	5vkcA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily	10 — Blc2-like

Domain ID domain_id	5vkcB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily	10 — Blc2-like

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Unit-cell length a length_a	63.920 Å
Unit-cell length b length_b	63.920 Å
Unit-cell length c length_c	91.400 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	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	22.810 Å
R factor r_factor	0.2020
R_work r_work	0.2010
R_free r_free	0.2220

Crystal structure of MCL-1 in complex with a BIM competitive inhibitor

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

Induced myeloid leukemia cell differentiation protein Mcl-1

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

5vkc__assembly_1__model_1

5vkc__assembly_1__model_1 | I(q)

5vkc__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of MCL-1 in complex with a BIM competitive inhibitor

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

Induced myeloid leukemia cell differentiation protein Mcl-1

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

5vkc__assembly_1__model_1

5vkc__assembly_1__model_1 | I(q)

5vkc__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)