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- PDB-1sps: BINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 ... -

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Basic information

Entry
Database: PDB / ID: 1sps
TitleBINDING OF A HIGH AFFINITY PHOSPHOTYROSYL PEPTIDE TO THE SRC SH2 DOMAIN: CRYSTAL STRUCTURES OF THE COMPLEXED AND PEPTIDE-FREE FORMS
Components
  • PEPTIDE YEEI
  • SRC SH2 DOMAIN
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


host cell membrane / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / ATP binding / membrane
Similarity search - Function
Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / SH2 domain / SHC Adaptor Protein / : ...Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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
Tyrosine-protein kinase transforming protein Src / Middle T antigen
Similarity search - Component
Biological speciesRous sarcoma virus
Hamster polyomavirus
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsWaksman, G. / Kuriyan, J.
CitationJournal: 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
DepositionMar 5, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Structure summary / Category: 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: SRC SH2 DOMAIN
D: PEPTIDE YEEI
B: SRC SH2 DOMAIN
E: PEPTIDE YEEI
C: SRC SH2 DOMAIN
F: PEPTIDE YEEI


Theoretical massNumber of molelcules
Total (without water)40,3326
Polymers40,3326
Non-polymers00
Water72140
1
A: SRC SH2 DOMAIN
D: PEPTIDE YEEI


Theoretical massNumber of molelcules
Total (without water)13,4442
Polymers13,4442
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-2 kcal/mol
Surface area6150 Å2
MethodPISA
2
B: SRC SH2 DOMAIN
E: PEPTIDE YEEI


Theoretical massNumber of molelcules
Total (without water)13,4442
Polymers13,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SRC SH2 DOMAIN
F: PEPTIDE YEEI


Theoretical massNumber of molelcules
Total (without water)13,4442
Polymers13,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.300, 93.300, 55.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: ILE D 7 - PRO D 8 OMEGA =210.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein SRC SH2 DOMAIN


Mass: 11970.480 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / References: UniProt: P00524
#2: Protein/peptide PEPTIDE YEEI


Mass: 1473.515 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hamster polyomavirus / Genus: Polyomavirus / References: UniProt: P03079
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal grow
*PLUS
pH: 8 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMHEPES1drop
25 mMEDTA1drop
35 mMdithiothreitol1drop
410 %PEG40001drop
530 %MPD1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. obs: 11714 / % possible obs: 89.1 % / Num. measured all: 19885 / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.18 / Rfactor obs: 0.18 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 12 120 3491
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_deg3.2
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 11420 / σ(I): 2 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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