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- PDB-1bkm: COCRYSTAL STRUCTURE OF D-AMINO ACID SUBSTITUTED PHOSPHOPEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bkm
TitleCOCRYSTAL STRUCTURE OF D-AMINO ACID SUBSTITUTED PHOSPHOPEPTIDE COMPLEX
ComponentsPP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN
KeywordsTRANSFORMING PROTEIN / V-SRC SH2 DOMAIN / PHOSPHOTYROSINE RECOGNITION DOMAIN / PP60 SRC SH2 DOMAIN / TRIPEPTIDE / D-AMINO ACID
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-1C5 / 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.Am.Chem.Soc. / Year: 1997
Title: Structure-Based Design of a Novel Series of Nonpeptide Ligands that Bind to the Pp60Src Sh2 Domain
Authors: Holland, D.R. / Lunney, E.A. / Plummer, M.S. / Mueller, W.T. / Mcconnell, P. / Pavlovsky, A. / Para, K.S. / Shahripour, A. / Humblet, C. / Sawyer, T.K. / Rubin, J.R.
#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
DepositionMay 2, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: 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: 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)13,4202
Polymers12,8211
Non-polymers5991
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.200, 46.900, 74.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12821.392 Da / Num. of mol.: 1 / Fragment: DOMAIN / Mutation: INS(G0,S1), INS(EFIVTD) AT C-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN STRAIN A / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P00524, EC: 2.7.1.112
#2: Chemical ChemComp-1C5 / [[O-PHOSPHONO-N-ACETYL-TYROSINYL]-GLUTAMYL-3[CYCLOHEXYLMETHYL]ALANINYL]-AMINE


Mass: 598.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H39N4O10P
#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 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 Å3/Da / Density % sol: 40.22 % / Description: WAKSMAN AND KURIYAN SRC SH2 STRUCTURE
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: 5% PEG 6K, 0.1M TRIS, PH 8, SITTING DROP EXPERIMENT, PROTEIN 50 MG/ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 8.0, vapor diffusion - sitting drop
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: 4 micro litter of protein solution was mixed with 2 micro litter of 5 solution and 4 micro litter of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
20.1 M1dropNaCl
30.01 MTris1drop
410 mM5 solution1drop
532 %PEG60001reservoir
60.1 MMES1reservoir

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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→25 Å / Num. obs: 6768 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.12 Å / Redundancy: 2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5 / % possible all: 71.9
Reflection shell
*PLUS
% possible obs: 71.9 %

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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
RfactorNum. reflection% reflectionSelection details
Rfree0.275 546 10 %RANDOM
Rwork0.2 ---
obs0.2 5528 --
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 0 61 874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.2
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→2.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.33 37 10 %
Rwork0.24 387 -
obs--50 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.7

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