1szm

DUAL BINDING MODE OF BISINDOLYLMALEIMIDE 2 TO PROTEIN KINASE A (PKA)

Method: X-RAY DIFFRACTION Dmax: 101.9 Å Quality: GOOD

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

cAMP-dependent protein kinase, alpha-catalytic subunit

Bos taurus

UniProt P00517

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–350 Mutation:V123A, L173M, Q181K Non-standard monomer:Yes (specific site not provided by mmCIF) BI4 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;278 K;LiCl, MesBisTris, methanol, MEGA-8, PKI(5-24), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 2.50 Å R-free 0.289
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–350 Mutation:V123A, L173M, Q181K Non-standard monomer:Yes (specific site not provided by mmCIF) BI4 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;278 K;LiCl, MesBisTris, methanol, MEGA-8, PKI(5-24), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 2.50 Å R-free 0.289

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.

97 other PDB entries and 110 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAPCA_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–350; UniProt 1–350 Author chain B; PDBConstruct 1–350; UniProt 1–350

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 1szm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1szm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1szm
Deposition date deposition_date2004-04-06
Structure title titleDUAL BINDING MODE OF BISINDOLYLMALEIMIDE 2 TO PROTEIN KINASE A (PKA)
Keywords keywordsPKA, PKC, bisindolyl maleimide 2, LY333531, selectivity, surrogate kinase, amino acid residue exchange, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.35
Radius of gyration Rg (electron density) rg_electron30.82
Forward intensity I(0) i082015300.00
Molecular weight molecular_weight74196.0 kDa
Excluded volume excluded_volume93761 ų
Envelope volume envelope_volume117900 ų
Hydration-shell volume shell_volume32827 ų
Envelope diameter envelope_diameter103.0
Shell Rg shell_rg36.79
Envelope Rg envelope_rg30.47
Shape Rg shape_rg30.82
Total Rg total_rg31.37
Total atoms total_atoms5247
Residues n_residues637
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 dmax101.9
Rg (real space) rg_real31.45
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real8.2020e+07
I(0) uncertainty (real space) i0_real_error1.2320e+06
Rg (reciprocal space) rg_reciprocal31.41
I(0) (reciprocal space) i0_reciprocal82010000.0000
Solution quality estimate total_estimate0.8829
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.0
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-0.562
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25200000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.902; Smooth: 0.897

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1szma_
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.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd1szmb_
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.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id1szmA01
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_id1szmA02
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_id1szmB01
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_id1szmB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1

8. Citations (2)

9. Files and Curves (10)