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1bak

SIGNAL TRANSDUCTION PLECKSTRIN HOMOLOGY DOMAIN OF G-PROTEIN COUPLED RECEPTOR KINASE 2 (BETA-ADRENERGIC RECEPTOR KINASE 1), C-TERMINAL EXTENDED, NMR, 20 STRUCTURES

Method: SOLUTION NMR Dmax: 66.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

G-PROTEIN COUPLED RECEPTOR KINASE 2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 556–670 Fragment：C-TERMINAL EXTENDED PLECKSTRIN HOMOLOGY DOMAIN Mutation：D552G, Y553S, A554H, L555M No other associated polymer SOLUTION NMR NMR measurement conditions：pH 4.5；308 K Resolution not provided

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.

Other PDB Difference from Current Entry 1BAK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3CIK Human GRK2 in Complex with Gbetagamma subunits Deposited 2008-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；277 K；200 mM NaCl, 5% ethylene glycol, 6.3% PEG 3350, pH 5.25, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.75 Å R-free 0.269
3KRW Human GRK2 in complex with Gbetgamma subunits and balanol (soak) Deposited 2009-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–689（688 aa）
Not recorded BA1 BALANOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；Well contained 100 mM MES, pH 5.6, 200 mM NaCl, 9% PEG 3350. Drops were 1 uL protein, 1 uL well, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.265
3KRX Human GRK2 in complex with Gbetgamma subunits and balanol (co-crystal) Deposited 2009-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–689（688 aa）
Not recorded BA1 BALANOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；Well contained 100 mM MES, pH 6.0, 200 mM NaCl, 9% PEG 3350. Drops were 1 uL protein, 1 uL well, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.270
3V5W Human G Protein-Coupled Receptor Kinase 2 in Complex with Soluble Gbetagamma Subunits and Paroxetine Deposited 2011-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Not recorded 8PR Paroxetine × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；100 mM MES pH 5.8, 200 mM NaCl, and 8% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.07 Å R-free 0.247
4MK0 Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally designed paroxetine derivative Deposited 2013-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 30–668（639 aa） Fragment：unp residues 30-668
Not recorded 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
4PNK G protein-coupled receptor kinase 2 in complex with GSK180736A Deposited 2014-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Not recorded KZQ (4S)-4-(4-fluorophenyl)-N-(2H-indazol-5-yl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；MES, PEG 3350, NaCl
Resolution 2.56 Å R-free 0.259
5HE1 Human GRK2 in complex with Gbetagamma subunits and CCG224062 Deposited 2016-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 29–670（642 aa） Fragment：UNP residues 29-670
Mutation：S670A ZS2 (4~{S})-4-[4-fluoranyl-3-(isoquinolin-1-ylmethylcarbamoyl)phenyl]-~{N}-(1~{H}-indazol-5-yl)-6-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-pyrimidine-5-carboxamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES, 0.8-1.2 M sodium chloride, 8-16% PEG3350
Resolution 3.15 Å R-free 0.250
5UKK Human GRK2 in complex with human G-beta-gamma subunits and CCG211998 (14ak) Deposited 2017-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 30–671（642 aa）
Mutation：S670A MG MAGNESIUM ION × 1 8DJ 5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluoro-N-[(pyridin-2-yl)methyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES, 8-16% PEG3350, 0.8-1.2 M sodium chloride
Resolution 2.60 Å R-free 0.281
5UKL Human GRK2 in complex with Gbetagamma subunits and CCG222886 (14bd) Deposited 2017-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 30–671（642 aa）
Mutation：S670A MG MAGNESIUM ION × 1 SIX 2-{5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluorophenyl}-N-[2-(1H-pyrazol-4-yl)ethyl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES, 0.8-1.2 M sodium chloride, 8-16% PEG3350
Resolution 2.15 Å R-free 0.228
5UUU Design, Synthesis, and Evaluation of the First Selective and Potent G-protein-Coupled Receptor Kinase 2 (GRK2) Inhibitor for the Potential Treatment of Heart Failure Deposited 2017-02-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–538（516 aa） Fragment：UNP residues 23-538
Not recorded QRW 3-({[4-methyl-5-(pyridin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)-N-[2-(trifluoromethyl)benzyl]benzamide × 1 SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；273 K；18% PEG MME 2000, 0.1 M MES pH 5.6, and 0.0175M Ammonium Sulfate
Resolution 2.70 Å R-free 0.257
5UVC Design, Synthesis, and Evaluation of the First Selective and Potent G-protein-Coupled Receptor Kinase 2 (GRK2) Inhibitor for the Potential Treatment of Heart Failure Deposited 2017-02-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–538（516 aa） Fragment：UNP residues 23-538
Not recorded 8PV N-benzyl-3-({[5-(pyridin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)benzamide × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；273 K；18% PEG MME 2000, 100mM MES pH 5.9, 17.5mM Ammonium Sulfate
Resolution 2.65 Å R-free 0.260
5WG3 Human GRK2 in complex with Gbetagamma subunits and CCG258748 Deposited 2017-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Not recorded AFM 2-fluoro-5-[(3S,4R)-3-{[(1H-indazol-5-yl)oxy]methyl}piperidin-4-yl]-N-[(1H-pyrazol-3-yl)methyl]benzamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES pH 6, 1.1 M NaCl, 8% PEG3350
Resolution 2.90 Å R-free 0.248
5WG4 Human GRK2 in complex with Gbetagamma subunits and CCG257284 Deposited 2017-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Not recorded AFV 2-fluoro-5-[(3S,4R)-3-{[(1H-indazol-5-yl)oxy]methyl}piperidin-4-yl]-N-[(pyridin-2-yl)methyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES pH 6, 6% PEG 3350, 1 M NaCl
Resolution 2.31 Å R-free 0.279
5WG5 Human GRK2 in complex with Gbetagamma subunits and CCG224061 Deposited 2017-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Not recorded ZSO 5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-2H-indazole × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES pH 6, 8-15% PEG3350, 0.8-1.2 M NaCl
Resolution 3.10 Å R-free 0.232
6C2Y Human GRK2 in complex with Gbetagamma subunits and CCG257142 Deposited 2018-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Mutation：S670A EJS (4R,5R,6S)-4-[4-fluoro-3-({[3-(methoxymethyl)-1,2,4-oxadiazol-5-yl]methyl}carbamoyl)phenyl]-N-(2H-indazol-5-yl)-6-methyl-2-oxohexahydropyrimidine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES pH 6.0, 800 mM NaCl, 8% PEG 3350
Resolution 2.74 Å R-free 0.292
6U7C Human GRK2 in complex with Gbetagamma subunits and CCG258747 Deposited 2019-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa）
Mutation：C68S Q1Y 5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluoro-N-[(2H-indazol-3-yl)methyl]benzamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；50 mM MES pH 6.0, 1.1 M NaCl, 6% PEG 3350
Resolution 2.44 Å R-free 0.262
7K7L Structure of a hit for G Protein Coupled Receptor Kinase 2 (GRK2) Inhibitor for the Potential Treatment of Heart Failure Deposited 2020-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 30–668（639 aa）
Not recorded MG MAGNESIUM ION × 1 W4D 3-benzyl-6-(1H-pyrazol-4-yl)quinazolin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；2% PEG 3350, 0.1M MES pH 6.5, 0.2M NaCl
Resolution 2.54 Å R-free 0.244
7K7Z Structure of a hit for G Protein Coupled Receptor Kinase 2 (GRK2) Inhibitor for the Potential Treatment of Heart Failure Deposited 2020-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 30–668（639 aa）
Not recorded W4G 3-benzyl-7-(1H-pyrazol-4-yl)quinazolin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；2% PEG 3350, 0.1M MES pH 6.5, 0.2M NaCl
Resolution 2.61 Å R-free 0.262
7PWD Structure of an inhibited GRK2-G-beta and G-gamma complex Deposited 2021-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–689（689 aa） Fragment：NONE
Mutation：S670A 8DS 4-chloranyl-N-[2-(4-chlorophenyl)ethyl]thieno[2,3-c]pyridine-2-carboxamide × 1 CL CHLORIDE ION × 2 1PE PENTAETHYLENE GLYCOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；ethylene glycol, PEG 3350, MES, NaCl
Resolution 2.60 Å R-free 0.230

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 5–119； UniProt 556–670

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 1bak

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1bak
Deposition date deposition_date1997-11-21
Structure title titleSIGNAL TRANSDUCTION PLECKSTRIN HOMOLOGY DOMAIN OF G-PROTEIN COUPLED RECEPTOR KINASE 2 (BETA-ADRENERGIC RECEPTOR KINASE 1), C-TERMINAL EXTENDED, NMR, 20 STRUCTURES
Keywords keywords;PLECKSTRIN HOMOLOGY DOMAIN, PH DOMAIN, SIGNAL TRANSDUCTION, G-BETA-GAMMA BINDING DOMAIN, BETA-ADRENERGIC RECEPTOR KINASE, BETA-ARK, G-PROTEIN COUPLED RECEPTOR KINASE (GRK-2), TRANSFERASE ;; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.43 Å
Radius of gyration Rg (electron density) rg_electron16.09 Å
Forward intensity I(0) i01155180000.00
Molecular weight molecular_weight283950.0 kDa
Excluded volume excluded_volume354370 ų
Envelope volume envelope_volume53785 ų
Hydration-shell volume shell_volume21312 ų
Envelope diameter envelope_diameter74.1 Å
Shell Rg shell_rg28.24 Å
Envelope Rg envelope_rg22.71 Å
Shape Rg shape_rg16.04 Å
Total Rg total_rg16.53 Å
Total atoms total_atoms39940
Residues n_residues2380
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax66.4 Å
Rg (real space) rg_real16.55 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real1.1550e+09
I(0) uncertainty (real space) i0_real_error1.5060e+07
Rg (reciprocal space) rg_reciprocal16.53 Å
I(0) (reciprocal space) i0_reciprocal1155000000.0000
Solution quality estimate total_estimate0.7449
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.7 Å
Skewness Skewness skewness0.613
Kurtosis Kurtosis kurtosis0.309
Angular range angular_range— – 0.4850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha577200.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.334; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.680; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1baka1
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)
Domain ID domain_idd1baka2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1bakA00
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)
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8. Citations (3)

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9. Files and Curves (10)