2wtk

Structure of the heterotrimeric LKB1-STRADalpha-MO25alpha complex

Method: X-RAY DIFFRACTION Dmax: 154.1 Å Quality: GOOD

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

CALCIUM-BINDING PROTEIN 39

HOMO SAPIENS

UniProt Q9Y376

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–341 Not recorded STE20-RELATED KINASE ADAPTER PROTEIN ALPHA × 1 (Q7RTN6) SERINE/THREONINE-PROTEIN KINASE 11 × 1 (Q15831) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;PH 8.5 Resolution 2.65 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–341 Not recorded STE20-RELATED KINASE ADAPTER PROTEIN ALPHA × 1 (Q7RTN6) SERINE/THREONINE-PROTEIN KINASE 11 × 1 (Q15831) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;PH 8.5 Resolution 2.65 Å R-free 0.291

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.

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAB39_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–341; UniProt 1–341 Author chain D; PDBConstruct 1–341; UniProt 1–341

STE20-RELATED KINASE ADAPTER PROTEIN ALPHA

HOMO SAPIENS

UniProt Q7RTN6

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 59–431 Fragment:PSEUDOKINASE DOMAIN, RESIDUES 59-431 CALCIUM-BINDING PROTEIN 39 × 1 (Q9Y376) SERINE/THREONINE-PROTEIN KINASE 11 × 1 (Q15831) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;PH 8.5 Resolution 2.65 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 59–431 Fragment:PSEUDOKINASE DOMAIN, RESIDUES 59-431 CALCIUM-BINDING PROTEIN 39 × 1 (Q9Y376) SERINE/THREONINE-PROTEIN KINASE 11 × 1 (Q15831) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;PH 8.5 Resolution 2.65 Å R-free 0.291

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STRAA_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–373; UniProt 59–431 Author chain E; PDBConstruct 1–373; UniProt 59–431

SERINE/THREONINE-PROTEIN KINASE 11

HOMO SAPIENS

UniProt Q15831

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 43–347 Fragment:KINASE DOMAIN, RESIDUES 43-347 Mutation:YES CALCIUM-BINDING PROTEIN 39 × 1 (Q9Y376) STE20-RELATED KINASE ADAPTER PROTEIN ALPHA × 1 (Q7RTN6) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;PH 8.5 Resolution 2.65 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 43–347 Fragment:KINASE DOMAIN, RESIDUES 43-347 Mutation:YES CALCIUM-BINDING PROTEIN 39 × 1 (Q9Y376) STE20-RELATED KINASE ADAPTER PROTEIN ALPHA × 1 (Q7RTN6) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;PH 8.5 Resolution 2.65 Å R-free 0.291

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STK11_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–305; UniProt 43–347 Author chain F; PDBConstruct 1–305; UniProt 43–347

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 2wtk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2wtk
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2wtk
Deposition date deposition_date2009-09-16
Structure title titleStructure of the heterotrimeric LKB1-STRADalpha-MO25alpha complex
Keywords keywords;TRANSFERASE-METAL-BINDING PROTEIN COMPLEX, TRANSFERASE METAL-BINDING PROTEIN COMPLEX, KINASE, NUCLEUS, SERINE/THREONINE-PROTEIN KINASE, PSEUDOKINASE, PHOSPHOPROTEIN, SIGNAL TRANSDUCTION, TRANSFERASE, NUCLEOTIDE-BINDING ;; TRANSFERASE/METAL-BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.47
Radius of gyration Rg (electron density) rg_electron45.60
Forward intensity I(0) i0617390000.00
Molecular weight molecular_weight209690.0 kDa
Excluded volume excluded_volume264410 ų
Envelope volume envelope_volume370920 ų
Hydration-shell volume shell_volume68414 ų
Envelope diameter envelope_diameter159.6
Shell Rg shell_rg49.71
Envelope Rg envelope_rg44.79
Shape Rg shape_rg45.61
Total Rg total_rg45.73
Total atoms total_atoms14748
Residues n_residues1818
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 dmax154.1
Rg (real space) rg_real45.67
Rg uncertainty (real space) rg_real_error1.71
I(0) (real space) i0_real6.1740e+08
I(0) uncertainty (real space) i0_real_error1.2670e+07
Rg (reciprocal space) rg_reciprocal45.47
I(0) (reciprocal space) i0_reciprocal617200000.0000
Solution quality estimate total_estimate0.8500
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.0
Skewness Skewness skewness0.422
Kurtosis Kurtosis kurtosis-0.520
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha81210000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.762; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.833

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2wtka_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.15 — Mo25 protein
Domain ID domain_idd2wtkc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd2wtkd_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.15 — Mo25 protein
Domain ID domain_idd2wtkf1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id2wtkA01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id2wtkB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2wtkB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id2wtkC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2wtkC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id2wtkD01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id2wtkE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2wtkE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id2wtkF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2wtkF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)