[English] 日本語
Yorodumi
- PDB-5j5s: Src kinase in complex with a sulfonamide inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j5s
TitleSrc kinase in complex with a sulfonamide inhibitor
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTransferase/Transferase Inhibitor / Protein kinase / inactive kinase / sulfonamide inhibitor / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein tyrosine kinase activity / protein phosphatase binding / mitochondrial inner membrane / cell differentiation / cytoskeleton / regulation of cell cycle / cell adhesion / endosome membrane / innate immune response / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
: / 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 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6G3 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsLebedev, I. / Feldman, H.C. / Georghiou, G. / Maly, D.J. / Seeliger, M.
CitationJournal: To Be Published
Title: Structural and Functional Analysis of the Allosteric Modulation of IRE1a with ATP-Competitive Kinase Inhibitors
Authors: Feldman, H.C. / Tong, M. / Wang, L. / Meza-Acevedo, R. / Gobillot, T.A. / Gliedt, M.J. / Hari, S.B. / Mitra, A.K. / Backes, B.J. / Papa, F.R. / Seeliger, M.A. / Maly, D.J.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4624
Polymers65,4532
Non-polymers1,0092
Water5,314295
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2312
Polymers32,7271
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2312
Polymers32,7271
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.210, 63.551, 73.664
Angle α, β, γ (deg.)100.60, 90.61, 90.96
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 32726.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-6G3 / N-{4-[8-amino-3-(propan-2-yl)imidazo[1,5-a]pyrazin-1-yl]naphthalen-1-yl}-N'-[3-(trifluoromethyl)phenyl]urea


Mass: 504.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H23F3N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7% PEG 5000MME, 100mM Bis-Tris pH 6, 1.5% Tacsimate pH 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.153→36.24 Å / Num. obs: 38412 / % possible obs: 94.2 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06834 / Net I/σ(I): 14.19
Reflection shellResolution: 2.153→2.23 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.2434 / Mean I/σ(I) obs: 6.43 / Num. measured obs: 15762 / Num. unique all: 3992 / % possible all: 87.83

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OIQ

2oiq


Resolution: 2.153→36.239 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1999 5.2 %0.2156
Rwork0.1669 ---
obs0.1695 38408 94.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.153→36.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 74 295 4499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084312
X-RAY DIFFRACTIONf_angle_d1.1255854
X-RAY DIFFRACTIONf_dihedral_angle_d13.911623
X-RAY DIFFRACTIONf_chiral_restr0.044619
X-RAY DIFFRACTIONf_plane_restr0.005743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1528-2.20660.27721320.20322372X-RAY DIFFRACTION85
2.2066-2.26620.24921390.19982575X-RAY DIFFRACTION94
2.2662-2.33290.23391470.18612667X-RAY DIFFRACTION96
2.3329-2.40820.2281480.17022657X-RAY DIFFRACTION97
2.4082-2.49420.22721420.16522712X-RAY DIFFRACTION97
2.4942-2.59410.21061470.16542676X-RAY DIFFRACTION98
2.5941-2.71210.20711520.17172688X-RAY DIFFRACTION98
2.7121-2.8550.21161470.17242720X-RAY DIFFRACTION98
2.855-3.03380.23711520.17682725X-RAY DIFFRACTION98
3.0338-3.26790.21651430.17612665X-RAY DIFFRACTION97
3.2679-3.59650.20511400.16172630X-RAY DIFFRACTION96
3.5965-4.11630.18661430.15312489X-RAY DIFFRACTION91
4.1163-5.18370.2231330.15072409X-RAY DIFFRACTION87
5.1837-36.24430.21361340.16892424X-RAY DIFFRACTION88
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)
13.07730.0378-1.66764.0244-0.07717.56430.0785-0.36290.06330.58740.0796-0.2093-0.16650.2479-0.07330.715-0.0521-0.02750.4413-0.00130.267210.051739.366822.3269
25.1619-0.2162-2.79562.066-2.36695.2776-0.07330.48410.1597-1.07520.46630.6139-0.0154-0.7349-0.23560.7582-0.0981-0.16020.53890.04640.42518.267542.931912.2735
37.2918-1.0852-0.14566.7973-1.52275.1166-0.1868-0.10170.57260.19070.21940.2087-0.8394-0.5293-0.03270.6940.1023-0.05970.4731-0.06960.29366.448341.0817.3849
45.501-1.1459-1.0034.73023.53886.1681-0.3946-0.54170.1696-0.259-0.26840.6185-0.1406-1.14240.52481.0124-0.26060.00320.9858-0.03860.6012-4.174731.890917.9933
51.7239-0.21060.22542.65491.78194.20470.0264-0.21810.08850.4793-0.0063-0.09290.2040.0684-0.01890.29230.0142-0.03730.25490.00780.3037.191831.28913.0182
63.67-0.924-0.7134.46540.3442.7732-0.00550.21450.0669-0.0864-0.12060.43930.0058-0.38130.0830.223-0.0208-0.03940.2558-0.01540.2991-2.160328.6545-12.1355
73.5370.9001-1.11583.60921.39892.88530.1080.52740.733-1.13350.19450.5838-1.6062-0.1379-0.25951.29230.1344-0.05050.57560.01880.54512.492471.6385-41.645
85.79342.17640.55019.7901-0.62125.92680.41650.29590.7922-0.4349-0.2906-0.7423-1.51650.9104-0.14731.1047-0.19510.10390.5333-0.03060.50127.815173.0517-38.3195
96.01111.0187-1.48035.5626-2.00775.95350.4238-0.00010.8447-0.1727-0.5594-1.0061-1.65631.04880.12371.0118-0.19590.01290.8076-0.01270.629217.707963.8162-39.4335
104.6548-1.8063-0.06236.6957-3.72732.45020.00510.49050.3661-1.2096-0.0098-0.3483-0.52250.3002-0.06820.9123-0.0834-0.00390.5088-0.07450.39388.003864.1307-37.9777
111.06020.3229-0.41652.76881.40374.2994-0.00680.07040.2319-0.2392-0.08250.372-0.3493-0.29590.05770.27390.029-0.05610.25050.01210.34084.039962.3771-20.68
122.93241.4087-0.52233.66050.24641.7377-0.0282-0.14430.06670.1127-0.0151-0.1434-0.07130.13360.02640.21890.0501-0.04230.24040.0260.259614.150360.9247-9.8217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 258 through 272 )
2X-RAY DIFFRACTION2chain 'A' and (resid 273 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 303 )
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 402 )
6X-RAY DIFFRACTION6chain 'A' and (resid 403 through 533 )
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 289 )
8X-RAY DIFFRACTION8chain 'B' and (resid 290 through 302 )
9X-RAY DIFFRACTION9chain 'B' and (resid 303 through 316 )
10X-RAY DIFFRACTION10chain 'B' and (resid 317 through 338 )
11X-RAY DIFFRACTION11chain 'B' and (resid 339 through 402 )
12X-RAY DIFFRACTION12chain 'B' and (resid 403 through 533 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more