3pk1

Crystal structure of Mcl-1 in complex with the BaxBH3 domain

Method: X-RAY DIFFRACTION Dmax: 78.2 Å Quality: GOOD

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

Induced myeloid leukemia cell differentiation protein Mcl-1

Homo sapiens

UniProt Q07820

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 174–326 Fragment:Mcl-1 Bcl-2 like region, UNP residues 174-326 Apoptosis regulator BAX × 1 (Q07812) CD CADMIUM ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;1M Sodium Acetate, 0.1M Hepes, 25mM Cadmium Sulfate, 5mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.49 Å R-free 0.245
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 174–326 Fragment:Mcl-1 Bcl-2 like region, UNP residues 174-326 Apoptosis regulator BAX × 1 (Q07812) CD CADMIUM ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;1M Sodium Acetate, 0.1M Hepes, 25mM Cadmium Sulfate, 5mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.49 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

141 other PDB entries and 284 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCL1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 37–189; UniProt 174–326 Author chain C; PDBConstruct 37–189; UniProt 174–326

Apoptosis regulator BAX

OrganismNot specified

UniProt Q07812

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 48–81 Fragment:BH3 domain, UNP residues 48-81 Induced myeloid leukemia cell differentiation protein Mcl-1 × 1 (Q07820) CD CADMIUM ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;1M Sodium Acetate, 0.1M Hepes, 25mM Cadmium Sulfate, 5mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.49 Å R-free 0.245
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 48–81 Fragment:BH3 domain, UNP residues 48-81 Induced myeloid leukemia cell differentiation protein Mcl-1 × 1 (Q07820) CD CADMIUM ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;1M Sodium Acetate, 0.1M Hepes, 25mM Cadmium Sulfate, 5mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.49 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

35 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BAX_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–34; UniProt 48–81 Author chain D; PDBConstruct 1–34; UniProt 48–81

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3pk1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3pk1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3pk1
Deposition date deposition_date2010-11-11
Structure title titleCrystal structure of Mcl-1 in complex with the BaxBH3 domain
Keywords keywordsBcl-2 family fold, Regulation of apoptosis, Bax, mitochondria, APOPTOSIS-APOPTOSIS REGULATOR complex; APOPTOSIS/APOPTOSIS REGULATOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.53
Radius of gyration Rg (electron density) rg_electron22.93
Forward intensity I(0) i031758100.00
Molecular weight molecular_weight40068.0 kDa
Excluded volume excluded_volume48432 ų
Envelope volume envelope_volume58934 ų
Hydration-shell volume shell_volume21925 ų
Envelope diameter envelope_diameter77.1
Shell Rg shell_rg29.34
Envelope Rg envelope_rg23.13
Shape Rg shape_rg23.00
Total Rg total_rg23.49
Total atoms total_atoms2691
Residues n_residues331
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.2
Rg (real space) rg_real23.56
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real3.1760e+07
I(0) uncertainty (real space) i0_real_error4.9380e+05
Rg (reciprocal space) rg_reciprocal23.56
I(0) (reciprocal space) i0_reciprocal31760000.0000
Solution quality estimate total_estimate0.8759
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.325
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4152000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3pk1A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily10 — Blc2-like
Domain ID domain_id3pk1C01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily10 — Blc2-like

8. Citations (1)

9. Files and Curves (10)