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- PDB-1skj: COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1skj
TitleCOCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX
ComponentsPP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN
KeywordsTYROSINE-PROTEIN KINASE / V-SRC SH2 DOMAIN / PHOSPHOTYROSINE RECOGNITION DOMAIN / PP60 SRC SH2 DOMAIN / PEPTIDOMIMETIC / UREIDO
Function / homology
Function and homology information


non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / ATP binding
Similarity search - Function
SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UR2 / Tyrosine-protein kinase transforming protein Src
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHolland, D.R. / Rubin, J.R.
Citation
Journal: J.Med.Chem. / Year: 1997
Title: Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand.
Authors: Plummer, M.S. / Holland, D.R. / Shahripour, A. / Lunney, E.A. / Fergus, J.H. / Marks, J.S. / McConnell, P. / Mueller, W.T. / Sawyer, T.K.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
Authors: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J.
History
DepositionSep 18, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4792
Polymers12,9081
Non-polymers5721
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.400, 74.400, 38.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN / SRC SH2


Mass: 12907.508 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN / Mutation: N-TERMINAL INS(GS) AND C-TERMINAL INS(EFIVTD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN STRAIN A / Cell line: JM 83 / Cell line (production host): JM83 / Production host: Escherichia coli (E. coli) / References: UniProt: P00524, EC: 2.7.1.112
#2: Chemical ChemComp-UR2 / 4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID


Mass: 571.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H38N3O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG-S-A-A-E- - : G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING : E-F-I-V-T-D NOT NATURAL ...G-S-A-A-E- - : G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING : E-F-I-V-T-D NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING

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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: 2.5 Å3/Da / Density % sol: 48.77 % / Description: WAKSMAN AND KURIYAN SRC SH2 STRUCTURE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 6K, 0.1M ODIUM CACODYLATE PH 6, HANGING DROP EXPERIMENT, PROTEIN 29 MG/ ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 6.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mM1drop1NaCl
210 mMTris-HCl1drop1pH7.
330 mg/mlprotein1drop1
420 %PEG60001drop2
5100 mMsodium cacodylate1drop2pH6.
64 mg/mlligand1drop3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationMonochromator: CU FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 4694 / % possible obs: 95.48 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 7 / % possible all: 96.9

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN MODEL FROM 1SPS

1sps


Resolution: 2→8 Å / Cross valid method: R-FREE / σ(F): 2.4
RfactorNum. reflection% reflectionSelection details
Rfree0.275 438 10 %RANDOM
Rwork0.2 ---
obs0.2 4253 89 %-
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms820 0 0 61 881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.7
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
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 53 10 %
Rwork0.24 445 -
obs--85 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.7

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