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1byg

KINASE DOMAIN OF HUMAN C-TERMINAL SRC KINASE (CSK) IN COMPLEX WITH INHIBITOR STAUROSPORINE

Method: X-RAY DIFFRACTION Dmax: 63.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (C-TERMINAL SRC KINASE)

Homo sapiens

UniProt P41240

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 173–450 Fragment：KINASE DOMAIN STU STAUROSPORINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；VAPOUR DIFFUSION, PROTEIN SOLUTION (10 MG/ML) CONTAINING 1MM STAUROSPORINE WAS MIXED IN 1:1 RATIO WITH THE RESERVOIR SOLUTION. THE RESERVOIR SOLUTION CONTAINED 0.2M MGCL2, 0.1M TRISHCL PH 9.0, 24% PEG 4000. Resolution 2.40 Å R-free 0.287

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 1BYG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–71（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.278
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–71（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.278
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–71（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.278
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–71（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.278
3D7T Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 188–450（263 aa） Fragment：Csk kinase domain
Mutation：K361A/K362A STU STAUROSPORINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；VAPOR DIFFUSION, SITTING DROP
Resolution 2.90 Å R-free 0.278
3D7T Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 188–450（263 aa） Fragment：Csk kinase domain
Mutation：K361A/K362A STU STAUROSPORINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；VAPOR DIFFUSION, SITTING DROP
Resolution 2.90 Å R-free 0.278
3D7U Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 188–450（263 aa） Fragment：Csk kinase domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.11 Å R-free 0.302
3D7U Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 188–450（263 aa） Fragment：Csk kinase domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.11 Å R-free 0.302
3EAC Crystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), Oxidized form. Deposited 2008-08-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 73–178（106 aa） Fragment：SH2 Domain (UNP residues 73 to 178)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.3；298 K；22% PEG 4000, 100 mM Bis-Tris, pH 7.3., EVAPORATION, temperature 298K
Resolution 1.37 Å R-free 0.217
3EAZ Crystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), C122S mutant. Deposited 2008-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 73–178（106 aa） Fragment：Csk, SH2 domain (UNP residues 73 to 178)
Mutation：C122S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；22% PEG 4000, 100 mM Bis-Tris, pH 7.3., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.31 Å R-free 0.226

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

View Construct and Data Evidence
UniProt name CSK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–278； UniProt 173–450

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 1byg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1byg
Deposition date deposition_date1998-10-14
Structure title titleKINASE DOMAIN OF HUMAN C-TERMINAL SRC KINASE (CSK) IN COMPLEX WITH INHIBITOR STAUROSPORINE
Keywords keywordsPROTEIN KINASE, C-TERMINAL SRC KINASE, PHOSPHORYLATION, STAUROSPORINE, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.71 Å
Radius of gyration Rg (electron density) rg_electron18.66 Å
Forward intensity I(0) i013339100.00
Molecular weight molecular_weight28248.0 kDa
Excluded volume excluded_volume35756 ų
Envelope volume envelope_volume41688 ų
Hydration-shell volume shell_volume18792 ų
Envelope diameter envelope_diameter65.4 Å
Shell Rg shell_rg24.95 Å
Envelope Rg envelope_rg18.98 Å
Shape Rg shape_rg18.62 Å
Total Rg total_rg19.73 Å
Total atoms total_atoms1988
Residues n_residues246
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 dmax63.6 Å
Rg (real space) rg_real19.65 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real1.3340e+07
I(0) uncertainty (real space) i0_real_error1.6550e+05
Rg (reciprocal space) rg_reciprocal19.66 Å
I(0) (reciprocal space) i0_reciprocal13340000.0000
Solution quality estimate total_estimate0.8074
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.291
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.4050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3862000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1byga_
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 (2 domains)

Domain ID domain_id1bygA01
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_id1bygA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)