[English] 日本語
Yorodumi
- PDB-5m0l: Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m0l
TitleCocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with the methylated Fasudil-derived fragment N-methylisoquinoline-5-sulfonamide (Ligand 02)
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsTRANSFERASE / PKA / Kinase / Fasudil-derivative / Inhibition / Cocrystal / 3x-Phosphorylated / Ligand 02
Function / homology
Function and homology information


negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus ...negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
~{N}-methylisoquinoline-5-sulfonamide / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.465 Å
AuthorsWienen-Schmidt, B. / Heine, A. / Klebe, G.
Funding support Belgium, 1items
OrganizationGrant numberCountry
European Research Council268145 - Project Acronym: DrugProfilBind Belgium
CitationJournal: To Be Published
Title: Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with different Fasudil-derivatives
Authors: Wienen-Schmidt, B. / Jonker, H. / Gerber, H.-D. / Saxena, K. / Kudlinzki, D. / Sreeramulu, S. / Heine, A. / Schwalbe, H. / Klebe, G.
History
DepositionOct 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9035
Polymers43,3402
Non-polymers5633
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-12 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.814, 79.707, 84.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylated at Ser11, Thr198, Ser339; the first 13 amino acids are not well defined in the electron density.
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Amino acids 5-24 from cAMP-dependent protein kinase inhibitor alpha from Sigma (order ID: P7739); the last two amino acids are not well defined in the crystal structure
Source: (synth.) Homo sapiens (human) / References: UniProt: P61925
#3: Chemical ChemComp-7CT / ~{N}-methylisoquinoline-5-sulfonamide


Mass: 222.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O2S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Drop: 10 mg/ml PKA (0.240 mM) 30 mM MBT (MES/Bis-Tris Puffer pH 6.9) 1 mM DTT 0.1 mM EDTA 75 mM LiCl 0.03 mM Mega 8 0.07mM PKI (Sigma: P7739) 1.2 mM ligand solved in DMSO (100 mM Stock) ...Details: Drop: 10 mg/ml PKA (0.240 mM) 30 mM MBT (MES/Bis-Tris Puffer pH 6.9) 1 mM DTT 0.1 mM EDTA 75 mM LiCl 0.03 mM Mega 8 0.07mM PKI (Sigma: P7739) 1.2 mM ligand solved in DMSO (100 mM Stock) Reservoir: 16% Methanol 0.003 mL drop volume, 0.4 mL reservoir volume

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.465→34.09 Å / Num. obs: 75918 / % possible obs: 98.7 % / Redundancy: 4.07 % / Rsym value: 0.041 / Net I/σ(I): 19.11
Reflection shellResolution: 1.465→1.55 Å / Redundancy: 4.18 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.7 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q8W

1q8w


Resolution: 1.465→32.907 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.59
RfactorNum. reflection% reflection
Rfree0.1728 3798 5 %
Rwork0.1525 --
obs0.1535 75917 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.465→32.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 38 390 3301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083092
X-RAY DIFFRACTIONf_angle_d1.0464208
X-RAY DIFFRACTIONf_dihedral_angle_d19.0521139
X-RAY DIFFRACTIONf_chiral_restr0.188445
X-RAY DIFFRACTIONf_plane_restr0.007569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4652-1.48380.24421320.23172501X-RAY DIFFRACTION94
1.4838-1.50330.22331390.21432642X-RAY DIFFRACTION98
1.5033-1.52390.22421380.20632616X-RAY DIFFRACTION98
1.5239-1.54570.20331390.19482625X-RAY DIFFRACTION99
1.5457-1.56870.1821400.19482678X-RAY DIFFRACTION98
1.5687-1.59320.2231390.17922603X-RAY DIFFRACTION99
1.5932-1.61940.21781370.17972645X-RAY DIFFRACTION99
1.6194-1.64730.18771410.16822654X-RAY DIFFRACTION98
1.6473-1.67720.19541360.17092594X-RAY DIFFRACTION98
1.6772-1.70950.16981390.15932629X-RAY DIFFRACTION98
1.7095-1.74440.19341390.15652636X-RAY DIFFRACTION99
1.7444-1.78230.18471400.16032690X-RAY DIFFRACTION99
1.7823-1.82380.17411390.15732623X-RAY DIFFRACTION99
1.8238-1.86940.18281420.1552676X-RAY DIFFRACTION99
1.8694-1.91990.18821390.16012665X-RAY DIFFRACTION99
1.9199-1.97640.19361410.15832660X-RAY DIFFRACTION99
1.9764-2.04020.18641400.15532686X-RAY DIFFRACTION99
2.0402-2.11310.18421440.15272714X-RAY DIFFRACTION99
2.1131-2.19770.16621410.14582695X-RAY DIFFRACTION100
2.1977-2.29770.15691410.1392667X-RAY DIFFRACTION100
2.2977-2.41880.16151420.14012712X-RAY DIFFRACTION99
2.4188-2.57030.16551430.14122711X-RAY DIFFRACTION99
2.5703-2.76860.17341430.15072690X-RAY DIFFRACTION99
2.7686-3.04710.16781430.15092734X-RAY DIFFRACTION99
3.0471-3.48760.17271440.15812744X-RAY DIFFRACTION99
3.4876-4.39230.16851470.13292760X-RAY DIFFRACTION99
4.3923-32.91530.14091500.14442869X-RAY DIFFRACTION98
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)
15.38763.8934-1.84226.4031-4.50773.4409-0.3648-1.01770.0670.7837-0.01560.25420.3562-0.14050.34120.35750.04850.08450.3353-0.0070.20348.9985-9.44225.9345
28.2261.9617-3.92851.9644-1.78732.49080.08080.18820.20950.0625-0.0288-0.1412-0.2602-0.0289-0.03830.15780.0058-0.01170.10360.02360.165617.0915-4.15-9.3723
35.0341.9868-1.00584.03530.80531.2484-0.14860.3089-0.3142-0.42210.1825-0.6040.0070.0755-0.05010.1670.00460.06330.2359-0.03560.242928.75-22.4503-23.8482
45.1308-5.0298-2.71165.51642.61381.4362-0.07080.73281.2115-0.971-0.4950.0797-1.3338-0.82060.26270.55790.1267-0.16020.36420.0090.513211.4154-24.0824-27.3917
57.6042-2.8935-0.01746.4617-2.70465.9928-0.1210.0994-0.1078-0.03610.1227-0.4013-0.11070.2118-0.04540.1378-0.0110.04980.1516-0.06280.182426.3111-26.8937-20.0423
63.1135-0.99481.27294.2906-0.61516.6780.13870.5856-0.0276-0.5874-0.28350.1058-0.2302-0.36390.18420.28840.01860.03670.3216-0.02590.149215.5691-16.6977-32.9858
71.2738-0.1897-0.38713.0813-2.53366.3727-0.00370.1390.034-0.1509-0.0261-0.09830.0229-0.07420.02920.08090.00640.01170.0972-0.00960.090513.8038-12.7969-17.6372
83.43031.9048-1.16613.9221-1.87451.40270.01550.2387-0.0431-0.13910.0025-0.27510.0116-0.0243-0.00850.13790.01880.04440.1536-0.02650.155122.7024-19.8781-21.7497
90.86080.43350.00361.02520.12170.698-0.00570.0369-0.118-0.02610.007-0.06180.06430.0291-0.00670.11810.00950.00540.10320.00160.11715.0569-25.4094-9.4858
101.8501-0.84830.34136.9397-0.44082.42720.02540.0931-0.026-0.20710.09440.16880.0011-0.0227-0.11270.1064-0.01260.00910.13310.01210.12788.8741-15.2715-16.5778
112.19520.02080.0340.8501-1.30952.0205-0.11630.27260.1795-0.15310.1149-0.1619-0.0449-0.10960.03970.15050.0212-0.01550.15580.03580.133-1.6698-12.4567-22.0386
126.9844-1.55093.40115.3199-2.46086.1584-0.08510.5050.381-0.290.10980.3855-0.09180.10950.04370.14110.0118-0.00860.16660.08040.1646-7.158-10.7323-21.036
132.30961.9157-0.33256.1396-1.14621.5796-0.05770.155-0.0203-0.1330.0101-0.00080.092-0.01030.03640.10470.00420.01070.1083-0.00540.0754-4.9301-24.4134-12.8888
141.43881.38241.84425.90860.93158.1335-0.26910.53080.0558-0.88440.42110.4895-0.0478-0.20660.01210.2426-0.0682-0.06140.26350.0260.1839-11.7067-24.7253-25.655
157.3716-3.8033.73313.3811-3.30133.316-0.03850.4741-0.049-0.17640.24250.44060.2064-0.7941-0.27020.1747-0.02460.00720.27690.00050.199-15.3732-29.6113-11.5314
162.50221.2480.4251.48760.30571.84910.0006-0.11160.30770.0332-0.05430.2212-0.1106-0.16020.060.11780.01490.0270.114-0.0250.1408-8.1528-19.0624-3.2455
171.15230.0405-1.57651.54592.7947.4307-0.1426-0.1592-0.38470.18590.0673-0.17790.49540.32180.02050.17410.0327-0.00930.15340.03830.253514.1727-32.2167-6.5975
182.68212.8567-2.61164.0021-3.57613.2016-0.10630.4219-0.2074-0.6843-0.0843-0.28760.1594-0.02130.32490.4288-0.00220.13750.4464-0.05440.224222.7774-22.6395-35.2503
193.42082.4458-1.99056.19930.34721.8626-0.08720.55220.3165-0.64540.0776-0.4313-0.16220.148-0.0060.23760.02680.0810.26860.07410.203920.0802-7.0526-29.4418
208.26753.1108-5.36823.8832-3.17025.4465-0.099-0.2980.06550.01240.0730.0654-0.00410.26090.03710.1938-0.01140.010.1492-0.05370.1642-8.9395-38.4487-21.2013
217.40262.49641.71983.54821.48411.3503-0.17290.4794-0.4685-0.30260.0749-0.0792-0.1758-0.07730.06340.2037-0.01330.02830.1661-0.05020.16352.1133-31.9464-24.2895
224.10913.8864-4.06743.6767-3.84944.059-0.53020.4159-0.1529-1.38740.1309-0.99370.4174-0.35890.47710.3774-0.01770.07820.2271-0.00730.25721.9022-24.2758-26.0163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 11:19)
2X-RAY DIFFRACTION2(chain A and resid 20:34)
3X-RAY DIFFRACTION3(chain A and resid 35:48)
4X-RAY DIFFRACTION4(chain A and resid 49:54)
5X-RAY DIFFRACTION5(chain A and resid 55:71)
6X-RAY DIFFRACTION6(chain A and resid 72:82)
7X-RAY DIFFRACTION7(chain A and resid 83:105)
8X-RAY DIFFRACTION8(chain A and resid 106:125)
9X-RAY DIFFRACTION9(chain A and resid 126:179)
10X-RAY DIFFRACTION10(chain A and resid 180:191)
11X-RAY DIFFRACTION11(chain A and resid 192:205)
12X-RAY DIFFRACTION12(chain A and resid 206:217)
13X-RAY DIFFRACTION13(chain A and resid 218:237)
14X-RAY DIFFRACTION14(chain A and resid 238:253)
15X-RAY DIFFRACTION15(chain A and resid 254:259)
16X-RAY DIFFRACTION16(chain A and resid 260:303)
17X-RAY DIFFRACTION17(chain A and resid 304:328)
18X-RAY DIFFRACTION18(chain A and resid 329:343)
19X-RAY DIFFRACTION19(chain A and resid 344:350)
20X-RAY DIFFRACTION20(chain B and resid 5:14)
21X-RAY DIFFRACTION21(chain B and resid 15:18)
22X-RAY DIFFRACTION22(chain B and resid 19:22)

+
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