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- PDB-1bbz: CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED... -

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Basic information

Entry
Database: PDB / ID: 1bbz
TitleCRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED HIGH-AFFINITY PEPTIDE LIGAND: IMPLICATIONS FOR SH3-LIGAND INTERACTIONS
Components
  • ABL TYROSINE KINASE
  • PEPTIDE P41
KeywordsCOMPLEX (TRANSFERASE/PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) / SIGNAL TRANSDUCTION / SH3 DOMAIN / COMPLEX (TRANSFERASE-PEPTIDE) complex
Function / homology
Function and homology information


: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process ...: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / cerebellum morphogenesis / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / regulation of cell motility / positive regulation of establishment of T cell polarity / activated T cell proliferation / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / negative regulation of mitotic cell cycle / regulation of Cdc42 protein signal transduction / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / syntaxin binding / alpha-beta T cell differentiation / positive regulation of dendrite development / positive regulation of cell migration involved in sprouting angiogenesis / peptidyl-tyrosine autophosphorylation / regulation of axon extension / regulation of T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of cell-cell adhesion / HDR through Single Strand Annealing (SSA) / neuromuscular process controlling balance / Myogenesis / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of vasoconstriction / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Bergmann glial cell differentiation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / myoblast proliferation / associative learning / negative regulation of cellular senescence / actin monomer binding / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / canonical NF-kappaB signal transduction / negative regulation of BMP signaling pathway / RHO GTPases Activate WASPs and WAVEs / cardiac muscle cell proliferation / ephrin receptor signaling pathway / positive regulation of T cell migration / endothelial cell migration / BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / cellular response to transforming growth factor beta stimulus / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / mismatch repair / ephrin receptor binding / four-way junction DNA binding / spleen development / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / phosphotyrosine residue binding / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / SH2 domain binding / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / protein kinase C binding / peptidyl-tyrosine phosphorylation / response to endoplasmic reticulum stress / thymus development / positive regulation of release of sequestered calcium ion into cytosol / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / post-embryonic development
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPisabarro, M.T. / Serrano, L. / Wilmanns, M.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions.
Authors: Pisabarro, M.T. / Serrano, L. / Wilmanns, M.
#1: Journal: Biochemistry / Year: 1996
Title: Rational Design of Specific High-Affinity Peptide Ligands for the Abl-SH3 Domain
Authors: Pisabarro, M.T. / Serrano, L.
#2: Journal: Nat.Struct.Biol. / Year: 1994
Title: High-Resolution Crystal Structures of Tyrosine Kinase SH3 Domains Complexed with Proline-Rich Peptides
Authors: Musacchio, A. / Saraste, M. / Wilmanns, M.
History
DepositionApr 28, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABL TYROSINE KINASE
B: PEPTIDE P41
C: ABL TYROSINE KINASE
D: PEPTIDE P41
E: ABL TYROSINE KINASE
F: PEPTIDE P41
G: ABL TYROSINE KINASE
H: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,21712
Polymers29,8338
Non-polymers3844
Water4,846269
1
A: ABL TYROSINE KINASE
B: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-24 kcal/mol
Surface area4020 Å2
MethodPISA
2
C: ABL TYROSINE KINASE
D: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-27 kcal/mol
Surface area4040 Å2
MethodPISA
3
E: ABL TYROSINE KINASE
F: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-27 kcal/mol
Surface area3960 Å2
MethodPISA
4
G: ABL TYROSINE KINASE
H: PEPTIDE P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5543
Polymers7,4582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-27 kcal/mol
Surface area4020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.680, 73.790, 80.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.997724, -0.067192, 0.005638), (0.011972, 0.094239, -0.995478), (0.066357, 0.993279, 0.094829)13.597, 53.0221, -22.2311
2given(0.999017, -0.043051, -0.010579), (-0.010289, 0.006953, -0.999923), (0.043121, 0.999049, 0.006503)13.343, 55.603, -20.7086
3given(0.999782, -0.018786, 0.009149), (-0.008709, 0.023367, 0.999689), (-0.018994, -0.99955, 0.023198)-11.2435, 20.0008, 55.7471
4given(0.999223, -0.006459, 0.03887), (-0.038098, 0.093375, 0.994902), (-0.010055, -0.99561, 0.093057)-12.1863, 17.2248, 54.3182
5given(0.998796, -0.035591, 0.033755), (-0.036358, -0.999088, 0.022386), (0.032927, -0.023586, -0.999179)-22.789, 76.9722, 35.5722
6given(0.999078, -0.033958, 0.026286), (-0.035198, -0.998215, 0.048245), (0.0246, -0.049125, -0.99849)-22.7921, 76.3346, 36.7642

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Components

#1: Protein
ABL TYROSINE KINASE


Mass: 6423.080 Da / Num. of mol.: 4 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00519
#2: Protein/peptide
PEPTIDE P41


Mass: 1035.149 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growMethod: vapor diffusion / pH: 3.1
Details: CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM ...Details: CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM CHLORIDE, AND 1MM DTT/EDTA. THE HANGING DROP CONTAINED 1:1 RATIO OF RESERVOIR AND PROTEIN-PEPTIDE SOLUTIONS., vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Mcitric acid1reservoir
22 Mammonium sulfate1reservoir
30.2 M1reservoirNaCl
41 mMdithiothreitol1reservoir
51 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.6→39.3 Å / Num. obs: 226846 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.59 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.58 / % possible all: 98.4
Reflection
*PLUS
Num. obs: 34430 / Num. measured all: 226846

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABO

1abo


Resolution: 1.65→8 Å / Cross valid method: FREE R-FACTOR / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.266 -10 %RANDOM
Rwork0.205 ---
obs0.205 31081 --
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 20 269 2415
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.678
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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