SAXSdb — 6oqd

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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 monomer	Monomer	Protein 1	;(4S,7aR,9aR,10S,15R)-6'-chloro-10-hydroxy-15-methyl-3',4',7a,8,9,9a,10,11,12,13,14,15-dodecahydro-2'H,3H,5H-spiro[1,19-(ethanediylidene)-16lambda~6~-cyclobuta[i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-4,1'-naphthalene]-16,16,18(7H,17H)-trione ; × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;(4S,7aR,9aR,10S,15R)-6'-chloro-10-hydroxy-15-methyl-3',4',7a,8,9,9a,10,11,12,13,14,15-dodecahydro-2'H,3H,5H-spiro[1,19-(ethanediylidene)-16lambda~6~-cyclobuta[i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-4,1'-naphthalene]-16,16,18(7H,17H)-trione ; × 2 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 1–157； UniProt 171–327

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	6oqd
Deposition date deposition_date	2019-04-26
Structure title title	Crystal structure of Mcl1 with inhibitor 8
Keywords keywords	protein-protein interaction, inhibitor, apoptosis, APOPTOSIS-INHIBITOR complex; APOPTOSIS/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.

6oqd__assembly_1__model_1

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

Download this curve (.dat)

6oqd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6oqd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.92 Å
Rg (electron density)	15.39 Å
Total Rg	16.57 Å
Atom count	1295
Residues	156
Excluded volume	23023 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6oqd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6oqd__assembly_2__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	Induced myeloid leukemia cell differentiation protein Mcl-1
Molecular weight formula_weight	17922.3 kDa
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	1466

EDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHVEDLEGG

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	;(4S,7aR,9aR,10S,15R)-6'-chloro-10-hydroxy-15-methyl-3',4',7a,8,9,9a,10,11,12,13,14,15-dodecahydro-2'H,3H,5H-spiro[1,19-(ethanediylidene)-16lambda~6~-cyclobuta[i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-4,1'-naphthalene]-16,16,18(7H,17H)-trione ;
Molecular weight formula_weight	587.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6oqda_
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

CATH v4.4 (1 domains)

Domain ID domain_id	6oqdA01
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	43.480 Å
Unit-cell length b length_b	89.664 Å
Unit-cell length c length_c	84.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.480 Å
Low-resolution limit resolution_low	44.830 Å
R factor r_factor	0.2030
R_work r_work	0.2013
R_free r_free	0.2351

Crystal structure of Mcl1 with inhibitor 8

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

6oqd__assembly_1__model_1

6oqd__assembly_1__model_1 | I(q)

6oqd__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Mcl1 with inhibitor 8

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

6oqd__assembly_1__model_1

6oqd__assembly_1__model_1 | I(q)

6oqd__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)