4mk0

Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally designed paroxetine derivative

Method: X-RAY DIFFRACTION Dmax: 145.7 Å Quality: REASONABLE

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

Beta-adrenergic receptor kinase 1

Homo sapiens

UniProt P25098

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 A; UniProt 30–668 Fragment:unp residues 30-668 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) GOL GLYCEROL × 1 29X 5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-1H-isoindol-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;277 K;6% PEG 3350, 1M NaCl, 2 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.238

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.

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARBK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–639; UniProt 30–668

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Bos taurus

UniProt P62871

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 B; UniProt 2–340 Not recorded Beta-adrenergic receptor kinase 1 × 1 (P25098) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) GOL GLYCEROL × 1 29X 5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-1H-isoindol-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;277 K;6% PEG 3350, 1M NaCl, 2 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.238

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.

72 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–339; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Bos taurus

UniProt P63212

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 G; UniProt 6–64 Not recorded Beta-adrenergic receptor kinase 1 × 1 (P25098) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) GOL GLYCEROL × 1 29X 5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-1H-isoindol-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;277 K;6% PEG 3350, 1M NaCl, 2 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.238

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.

215 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 1–59; UniProt 6–64

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 4mk0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4mk0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4mk0
Deposition date deposition_date2013-09-04
Structure title titleCrystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally designed paroxetine derivative
Keywords keywords;INHIBITOR COMPLEX, PROTEIN KINASE, HYDROLASE, ATP BINDING, PHOSPHORYLATION, PERIPHERAL MEMBRANE PROTEIN, SIGNALING PROTEIN-inhibitor complex ;; SIGNALING PROTEIN/inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.43
Radius of gyration Rg (electron density) rg_electron42.49
Forward intensity I(0) i0213523000.00
Molecular weight molecular_weight117540.0 kDa
Excluded volume excluded_volume146430 ų
Envelope volume envelope_volume204200 ų
Hydration-shell volume shell_volume42520 ų
Envelope diameter envelope_diameter147.9
Shell Rg shell_rg44.30
Envelope Rg envelope_rg41.68
Shape Rg shape_rg42.48
Total Rg total_rg42.64
Total atoms total_atoms8251
Residues n_residues1029
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 dmax145.7
Rg (real space) rg_real42.78
Rg uncertainty (real space) rg_real_error1.21
I(0) (real space) i0_real2.1350e+08
I(0) uncertainty (real space) i0_real_error3.8580e+06
Rg (reciprocal space) rg_reciprocal42.44
I(0) (reciprocal space) i0_reciprocal213400000.0000
Solution quality estimate total_estimate0.5834
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.4
Skewness Skewness skewness0.432
Kurtosis Kurtosis kurtosis-0.672
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha24280000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 0.016; Positv: 1.000; Valcen: 0.681; Smooth: 0.786

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id4mk0A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily1270
Domain ID domain_id4mk0A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology167 — Regulator of G-protein Signalling 4; domain 2
Homologous superfamily homologous superfamily10 — Regulator of G-protein Signalling 4, domain 2
Domain ID domain_id4mk0A03
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_id4mk0A04
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_id4mk0A05
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id4mk0B00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id4mk0G00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain

8. Citations (1)

9. Files and Curves (10)