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- PDB-3zmq: Src-derived mutant peptide inhibitor complex of PTP1B -

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Basic information

Entry
Database: PDB / ID: 3zmq
TitleSrc-derived mutant peptide inhibitor complex of PTP1B
Components
  • PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
  • TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / TRANSFERASE
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of telomere maintenance / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of telomere maintenance / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / negative regulation of focal adhesion assembly / positive regulation of integrin activation / positive regulation of protein processing / Activated NTRK2 signals through FYN / BMP receptor binding / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / Netrin mediated repulsion signals / negative regulation of neutrophil activation / focal adhesion assembly / connexin binding / osteoclast development / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / regulation of vascular permeability / signal complex assembly / branching involved in mammary gland duct morphogenesis / positive regulation of small GTPase mediated signal transduction / Co-stimulation by CD28 / EPH-Ephrin signaling / positive regulation of podosome assembly / DCC mediated attractive signaling / positive regulation of lamellipodium morphogenesis / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / podosome / odontogenesis / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / PTK6 Down-Regulation / Regulation of KIT signaling / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / Signaling by ALK / regulation of early endosome to late endosome transport / leukocyte migration / insulin receptor recycling / phospholipase activator activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / GP1b-IX-V activation signalling / EPHA-mediated growth cone collapse / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / Co-inhibition by CTLA4 / p130Cas linkage to MAPK signaling for integrins / oogenesis / interleukin-6-mediated signaling pathway / Receptor Mediated Mitophagy / stress fiber assembly / positive regulation of Notch signaling pathway / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / Signaling by EGFR / negative regulation of vascular associated smooth muscle cell migration / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / stimulatory C-type lectin receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / RUNX2 regulates osteoblast differentiation / regulation of type I interferon-mediated signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of MAP kinase activity / regulation of cell-cell adhesion / forebrain development / uterus development / negative regulation of intrinsic apoptotic signaling pathway / PECAM1 interactions / vascular endothelial cell response to oscillatory fluid shear stress / GRB2:SOS provides linkage to MAPK signaling for Integrins / peptidyl-tyrosine dephosphorylation / Recycling pathway of L1 / positive regulation of systemic arterial blood pressure / RHOU GTPase cycle / regulation of endocytosis / regulation of heart rate by cardiac conduction / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / protein tyrosine kinase activator activity / RET signaling / signaling receptor activator activity / negative regulation of anoikis / cellular response to angiotensin / FCGR activation / regulation of proteolysis / positive regulation of epithelial cell migration
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / : / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / : / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTemmerman, K. / Pogenberg, V. / Meyer, C. / Koehn, M. / Wilmanns, M.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Development of Accessible Peptidic Tool Compounds to Study the Phosphatase Ptp1B in Intact Cells.
Authors: Meyer, C. / Hoeger, B. / Temmerman, K. / Tatarek-Nossol, M. / Pogenberg, V. / Bernhagen, J. / Wilmanns, M. / Kapurniotu, A. / Kohn, M.
History
DepositionFeb 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
C: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC


Theoretical massNumber of molelcules
Total (without water)39,7102
Polymers39,7102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5.4 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.020, 61.270, 88.690
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 TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1 / PROTEIN-TYROSINE PHOSPHATASE 1B / PTP-1B


Mass: 38447.793 Da / Num. of mol.: 1
Fragment: TYROSINE-PROTEIN PHOSPHATASE DOMAIN, RESIDUES 1-321
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Protein/peptide PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC / PROTO-ONCOGENE C-SRC / PP60C-SRC / P60-SRC


Mass: 1262.167 Da / Num. of mol.: 1
Fragment: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC RESIDUES 527-536
Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P12931, non-specific protein-tyrosine kinase
Has protein modificationY
Sequence detailsRESIDUES 527-536, WITH P528A

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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: 2.09 Å3/Da / Density % sol: 41.08 % / Description: NONE
Crystal growDetails: 0.2M MGCL2, 0.1M TRIS-HCL, PH=8.5 30% (W/V)POLYETHYLENE GLYCOL 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2012 / Details: KB MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→50.41 Å / Num. obs: 5375 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 44.62 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 7.3
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A5K

3a5k


Resolution: 3.3→50.271 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 29.4 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.3044 242 4.5 %
Rwork0.2478 --
obs0.2504 5342 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.2 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 0 1939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011986
X-RAY DIFFRACTIONf_angle_d1.4182716
X-RAY DIFFRACTIONf_dihedral_angle_d18.763670
X-RAY DIFFRACTIONf_chiral_restr0.081310
X-RAY DIFFRACTIONf_plane_restr0.013347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-4.15770.33381190.26212504X-RAY DIFFRACTION100
4.1577-50.27680.28361230.23722596X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06551.04980.81222.1142-0.53133.0050.1163-0.60140.53920.2078-0.2309-1.0384-0.08810.20920.25870.5235-0.0933-0.10390.5822-0.11010.4099-4.802116.5222-0.8588
23.1344-0.09320.51653.5346-0.67084.2078-0.2163-0.29-0.50550.43770.0872-0.10560.4254-0.0296-0.07370.65230.07720.07050.38820.04880.4135-7.0354-7.3705-9.8426
32.86260.44270.8583.0271-0.33823.4013-0.20140.06620.0456-0.8629-0.0641-0.29720.0249-0.54-0.03480.31970.05170.02560.4137-0.01790.345-14.08520.4996-13.1041
42.28710.37370.84821.12850.10363.3516-0.06630.3633-0.3492-1.07210.0381-0.240.57510.3883-0.02890.71120.00250.03910.4127-0.00010.3797-13.5722-1.049-28.8903
52.61920.67380.95953.5679-0.00493.64850.0588-0.16860.1155-0.5984-0.2782-0.08640.11780.11090.09240.3567-0.01010.06590.3205-0.0030.2569-13.512510.6068-24.1995
62.49570.58541.01782.704-0.58462.90290.1114-0.30180.57580.0192-0.20590.0802-0.2839-0.57160.11950.39060.08350.07230.4049-0.04830.2862-16.659612.6517-11.5362
72.98520.46950.94761.6236-0.25613.231-0.16220.09150.310.4472-0.1360.2577-0.8960.35560.25530.36150.06880.03890.3632-0.01370.3028-8.939617.4047-10.524
83.78740.09050.87593.9178-1.39024.3781-0.25040.06460.2961-0.3524-0.6263-0.6881-0.09450.8670.18120.5339-0.05240.01950.90430.07390.74583.53153.6485-11.4496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 7 THROUGH 32 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 33 THROUGH 63 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 64 THROUGH 90 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 91 THROUGH 162 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 163 THROUGH 201 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 202 THROUGH 255 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 256 THROUGH 279 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 1 THROUGH 6 )

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