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- PDB-3zmp: Src-derived peptide inhibitor complex of PTP1B -

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Basic information

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


regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / response to mineralocorticoid / positive regulation of dephosphorylation / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / entry of bacterium into host cell / positive regulation of protein transport / Regulation of gap junction activity / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / regulation of vascular permeability / Activated NTRK2 signals through FYN / positive regulation of integrin activation / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / : / intestinal epithelial cell development / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / response to acidic pH / focal adhesion assembly / signal complex assembly / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / podosome / regulation of bone resorption / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / adherens junction organization / DCC mediated attractive signaling / myoblast proliferation / EPH-Ephrin signaling / odontogenesis / negative regulation of mitochondrial depolarization / Ephrin signaling / cellular response to peptide hormone stimulus / osteoclast development / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / Receptor Mediated Mitophagy / regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / CTLA4 inhibitory signaling / GP1b-IX-V activation signalling / oogenesis / interleukin-6-mediated signaling pathway / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / leukocyte migration / phospholipase activator activity / insulin receptor recycling / DNA biosynthetic process / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of hippo signaling / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / positive regulation of Notch signaling pathway / negative regulation of PERK-mediated unfolded protein response / Signaling by EGFR / cellular response to platelet-derived growth factor stimulus / negative regulation of vascular endothelial growth factor receptor signaling pathway / stress fiber assembly / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / progesterone receptor signaling pathway / RUNX2 regulates osteoblast differentiation / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / dendritic growth cone / sorting endosome / mitochondrial crista
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, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...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 / Tyrosine specific protein phosphatases domain profile. / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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: 2.619 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 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_dist_value / _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

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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
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
C: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
D: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC


Theoretical massNumber of molelcules
Total (without water)79,4724
Polymers79,4724
Non-polymers00
Water77543
1
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
D: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC


Theoretical massNumber of molelcules
Total (without water)39,7362
Polymers39,7362
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-8 kcal/mol
Surface area11880 Å2
MethodPISA
2
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
C: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC


Theoretical massNumber of molelcules
Total (without water)39,7362
Polymers39,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6.8 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 88.070, 91.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9973, -0.00746, 0.07318), (0.007593, -1, 0.001538), (0.07317, 0.00209, 0.9973)
Vector: 36.81, -6.992, -2.948)

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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.: 2
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 / SRC-DERIVED PEPTIDE / PROTO-ONCOGENE C-SRC / PP60C-SRC / P60-SRC


Mass: 1288.204 Da / Num. of mol.: 2 / Fragment: RESIDUES 527-536 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 527-536

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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: 1.81 Å3/Da / Density % sol: 31.88 % / Description: NONE
Crystal growDetails: 0.2M MGCL2, 27.14W/V% PEG3350, 0.1M HEPES, PH=7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2012 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→100 Å / Num. obs: 17923 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 12 % / Biso Wilson estimate: 36.77 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 10.74
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

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

3a5k


Resolution: 2.619→63.616 Å / SU ML: 0.39 / σ(F): 1.13 / Phase error: 29.29 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2707 1692 5.1 %
Rwork0.2201 --
obs0.2228 17814 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.619→63.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 0 43 4376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014433
X-RAY DIFFRACTIONf_angle_d1.3376022
X-RAY DIFFRACTIONf_dihedral_angle_d15.921617
X-RAY DIFFRACTIONf_chiral_restr0.086664
X-RAY DIFFRACTIONf_plane_restr0.009774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6188-2.69590.36471520.31672650X-RAY DIFFRACTION100
2.6959-2.78290.37331740.31112571X-RAY DIFFRACTION100
2.7829-2.88230.3641100.30052667X-RAY DIFFRACTION100
2.8823-2.99770.31161320.29342601X-RAY DIFFRACTION99
2.9977-3.13420.30621630.26752647X-RAY DIFFRACTION99
3.1342-3.29940.3121500.24432605X-RAY DIFFRACTION99
3.2994-3.50610.28871310.22112623X-RAY DIFFRACTION100
3.5061-3.77680.24781310.19752643X-RAY DIFFRACTION99
3.7768-4.15680.23931380.17932639X-RAY DIFFRACTION99
4.1568-4.75810.21261350.16412612X-RAY DIFFRACTION99
4.7581-5.9940.21851340.1812640X-RAY DIFFRACTION100
5.994-63.63460.24731420.19642637X-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)
11.68250.4242-1.85253.7603-0.87712.41350.00250.6714-0.1834-1.48790.39020.13710.7015-0.4965-0.29011.2562-0.1595-0.05150.6281-0.03190.6321.3198-24.8214-45.9361
24.10270.6028-1.13656.78090.24892.5281-0.0977-0.1024-0.30970.15730.09230.75510.139-0.2317-0.06710.32050.0108-0.0510.23590.03250.3585-4.7812-12.6416-23.3187
34.0144-1.001-1.67646.7217-0.14192.4374-0.06210.09920.0173-0.1543-0.12850.1737-0.3048-0.3650.13410.399-0.0271-0.06090.33190.02290.5844-0.34072.1131-24.7856
43.74340.1258-0.86166.13680.99134.3016-0.23580.2666-0.1001-1.00650.0238-0.50310.36820.17570.18230.512-0.0290.04490.27470.0240.37318.0471-14.3555-36.817
53.5179-0.22150.83135.6106-0.87054.0750.44970.96140.768-1.9557-0.0827-0.15210.04850.70940.02421.29120.20880.29750.58080.1811.258333.552518.8451-43.7053
63.02740.53971.52584.8409-0.52323.01140.053-0.27710.21220.7045-0.2781-1.4951-0.05980.19230.34650.50080.0199-0.15440.28310.02810.767140.02016.1375-23.1976
73.4209-1.37861.75843.3665-3.576.8769-0.0559-0.2467-0.11780.4327-0.08-0.38740.20460.0590.18970.61530.0139-0.08810.3204-0.04240.827835.7659-11.0621-20.2317
81.8346-0.19690.41937.0086-0.86932.92780.20780.2430.1043-1.308-0.2631-0.3044-0.002-0.08120.05740.50920.10960.01870.3068-0.02740.35427.8836.1145-36.2485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:31)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 32:125)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 126:187)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 188:283)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 3:31)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 32:125)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 126:171)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 172:278)

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