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- PDB-2v76: Crystal structure of the human dok1 PTB domain -

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Basic information

Entry
Database: PDB / ID: 2v76
TitleCrystal structure of the human dok1 PTB domain
ComponentsDOCKING PROTEIN 1
KeywordsPROTEIN BINDING / PROTEIN-BINDING / PTB DOMAIN / PHOSPHORYLATION / ADAPTOR PROTEIN
Function / homology
Function and homology information


macrophage colony-stimulating factor signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / RET signaling / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / Ras protein signal transduction / cell surface receptor signaling pathway / perinuclear region of cytoplasm / signal transduction ...macrophage colony-stimulating factor signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / RET signaling / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / Ras protein signal transduction / cell surface receptor signaling pathway / perinuclear region of cytoplasm / signal transduction / nucleus / cytosol
Similarity search - Function
Dok1/2/3, PTB domain / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain ...Dok1/2/3, PTB domain / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Docking protein 1 / Docking protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOxley, C.L. / Anthis, N.J. / Lowe, E.D. / Campbell, I.D. / Wegener, K.L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: An Integrin Phosphorylation Switch: The Effect of {Beta}3 Integrin Tail Phosphorylation on Dok1 and Talin Binding.
Authors: Oxley, C.L. / Anthis, N.J. / Lowe, E.D. / Vakonakis, I. / Campbell, I.D. / Wegener, K.L.
History
DepositionJul 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DOCKING PROTEIN 1
B: DOCKING PROTEIN 1
C: DOCKING PROTEIN 1
D: DOCKING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,19814
Polymers48,0584
Non-polymers1,13910
Water6,972387
1
A: DOCKING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3234
Polymers12,0151
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DOCKING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4114
Polymers12,0151
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: DOCKING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2033
Polymers12,0151
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: DOCKING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2613
Polymers12,0151
Non-polymers2462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.880, 100.168, 67.101
Angle α, β, γ (deg.)90.00, 117.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DOCKING PROTEIN 1 / DOWNSTREAM OF TYROSINE KINASE 1 / P62 / DOK / PP62 / HUMAN DOK1 PTB


Mass: 12014.623 Da / Num. of mol.: 4 / Fragment: PTB DOMAIN, RESIDUES 152-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q53TY2, UniProt: Q99704*PLUS

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Non-polymers , 5 types, 397 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE
Crystal growpH: 7.5
Details: 2M AMONIUM SULFATE, 2% PEG 400, 0.1M NA HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: Sep 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→25.98 Å / Num. obs: 59364 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALACCP4data scaling
PHASERCCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P5T

1p5t


Resolution: 1.6→59.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.871 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2997 5 %RANDOM
Rwork0.188 ---
obs0.19 56366 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.46 Å2
2---0.61 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.6→59.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 70 387 3666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9544585
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44821.916167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69815550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9961541
X-RAY DIFFRACTIONr_chiral_restr0.1130.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022579
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21545
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22308
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4540.2125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6141.52057
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34123243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.38631496
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9444.51333
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 209
Rwork0.257 4086

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