[English] 日本語
Yorodumi
- PDB-4uja: Protein Kinase A in complex with an Inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uja
TitleProtein Kinase A in complex with an Inhibitor
Components
  • CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
  • PEPTIDE
KeywordsTRANSFERASE
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / channel activator activity / negative regulation of cAMP-dependent protein kinase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / channel activator activity / negative regulation of cAMP-dependent protein kinase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / 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 / Loss of phosphorylation of MECP2 at T308 / negative regulation of interleukin-2 production / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of protein import into nucleus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / Triglyceride catabolism / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / RET signaling / cAMP/PKA signal transduction / Interleukin-3, Interleukin-5 and GM-CSF signaling / plasma membrane raft / PKA activation in glucagon signalling / Regulation of MECP2 expression and activity / DARPP-32 events / regulation of cardiac conduction / regulation of macroautophagy / regulation of cardiac muscle contraction / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / Ion homeostasis / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / sperm midpiece / regulation of proteasomal protein catabolic process / cellular response to epinephrine stimulus / calcium channel complex / positive regulation of gluconeogenesis / Mitochondrial protein degradation / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / acrosomal vesicle / CD209 (DC-SIGN) signaling / positive regulation of calcium-mediated signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of heart rate / FCGR3A-mediated IL10 synthesis / protein export from nucleus / positive regulation of phagocytosis / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / Regulation of insulin secretion / neuromuscular junction / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / positive regulation of cholesterol biosynthetic process / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / peptidyl-serine phosphorylation / VEGFA-VEGFR2 Pathway / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytokine-mediated signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / Regulation of PLK1 Activity at G2/M Transition / GPER1 signaling / manganese ion binding
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
Chem-4L7 / BROMIDE ION / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsAlam, K.A. / Engh, R.A.
CitationJournal: Chemistry / Year: 2016
Title: Addressing the Glycine-Rich Loop of Protein Kinases by a Multi-Facetted Interaction Network: Inhibition of Pka and a Pkb Mimic.
Authors: Lauber, B.S. / Hardegger, L.A. / Asraful, A.K. / Lund, B.A. / Dumele, O. / Harder, M. / Kuhn, B. / Engh, R.A. / Diederich, F.
History
DepositionApr 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Jan 10, 2024Group: 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
B: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6375
Polymers43,0352
Non-polymers6023
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-11.8 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.240, 74.920, 80.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA / PKA C-ALPHA / PKA


Mass: 40808.570 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 1-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide PEPTIDE


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925*PLUS

-
Non-polymers , 4 types, 297 molecules

#3: Chemical ChemComp-4L7 / 7-{(3S,4R)-4-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}quinazolin-4(3H)-one


Mass: 404.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14BrN3O2S
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Nonpolymer detailsPHOSPHOSERINE (SEP): PHOSPHOSERINE (4S)-2-METHYL-2,4-PENTANEDIOL (MPD): MPD (4S)-2-METHYL-2,4- ...PHOSPHOSERINE (SEP): PHOSPHOSERINE (4S)-2-METHYL-2,4-PENTANEDIOL (MPD): MPD (4S)-2-METHYL-2,4-PENTANEDIOL (DRG): DRG PHOSPHOTHREONINE (TPO): PHOSPHOTHREONINE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.12 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10MG/ML PROTEIN, 25MM BISTRIS/MES PH6.9, 50MM KCL, 1.5MM OCTANOYL-N-METHYLGLUCAMIDE, 1MM PROTEIN KINASE INHIBITOR PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

-
Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
DetectorDate: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.93→43.61 Å / Num. obs: 30034 / % possible obs: 90.1 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 25.34 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.95
Reflection shellResolution: 1.93→2 Å / Redundancy: 1.9 % / % possible all: 90.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VQH

3vqh


Resolution: 1.93→43.607 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 1543 5.1 %
Rwork0.1637 --
obs0.166 30034 90.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→43.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 33 294 3259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.033047
X-RAY DIFFRACTIONf_angle_d1.2494121
X-RAY DIFFRACTIONf_dihedral_angle_d14.0551145
X-RAY DIFFRACTIONf_chiral_restr0.043433
X-RAY DIFFRACTIONf_plane_restr0.008545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.99230.30761330.24262616X-RAY DIFFRACTION92
1.9923-2.06350.25411590.20992623X-RAY DIFFRACTION93
2.0635-2.14610.2291410.18572628X-RAY DIFFRACTION93
2.1461-2.24380.24021320.18222579X-RAY DIFFRACTION91
2.2438-2.36210.21961430.16672610X-RAY DIFFRACTION92
2.3621-2.51010.20661420.16562622X-RAY DIFFRACTION92
2.5101-2.70390.2171400.17492558X-RAY DIFFRACTION90
2.7039-2.97590.24831420.16752602X-RAY DIFFRACTION90
2.9759-3.40640.20971240.15552565X-RAY DIFFRACTION89
3.4064-4.29110.15231430.14192554X-RAY DIFFRACTION88
4.2911-43.61840.18831440.14942534X-RAY DIFFRACTION83
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)
11.2698-0.1998-0.53961.1070.51720.40350.09750.1978-0.1381-0.4128-0.00990.50870.3598-0.49660.17980.2927-0.0853-0.10970.3927-0.02710.2952-39.7807-1.2532-17.6424
20.52070.2621-0.02840.5073-0.27260.1798-0.0754-0.15810.09840.1323-0.01140.1004-0.209-0.1201-0.03150.13210.0586-0.02030.2239-0.02690.2283-31.920.4097-1.66
30.1347-0.00740.12570.0577-0.09240.248-0.0160.01790.31170.04890.05370.0954-0.1928-0.17110.00020.11950.01120.01070.2245-0.01670.2254-30.239419.56090.0615
40.102-0.19840.00820.67790.25190.7790.01530.13890.066-0.0864-0.03360.09240.0192-0.19570.00010.15150.0083-0.01860.2015-0.01850.2126-29.848511.931-9.2196
50.03370.0276-0.08270.25120.03450.2456-0.0381-0.11060.04510.03690.05380.08760.0877-0.139-00.17050.00840.01610.2319-0.01430.1946-28.9114.71257.2145
60.5059-0.00280.24820.7376-0.41340.5717-0.01730.0687-0.0693-0.1034-0.03710.02310.2536-0.0559-0.00010.1778-0.00820.01890.1684-0.02350.1442-24.8608-3.5037-4.5181
70.01930.1113-0.10290.9047-0.27430.9978-0.01350.0063-0.2473-0.136-0.0442-0.31840.5150.22080.02980.30060.05840.03520.1560.02860.2039-14.4344-13.13253.645
82.4141-0.4080.93950.5153-0.45350.56040.07020.4457-0.4976-0.04760.0169-0.00240.73490.04310.07450.5091-0.00650.01340.2234-0.0820.2657-25.4187-17.521-8.1374
90.17730.07030.22580.34660.05310.2919-0.10970.02090.02090.24180.00830.28160.1484-0.2803-0.03090.3065-0.1340.04590.2794-0.00040.2725-41.0392-9.07893.6737
100.4263-0.56930.01390.936-0.12060.4685-0.0270.00670.14030.01320.0332-0.0388-0.302-0.0885-0.00750.20320.013-0.01740.1927-0.02550.2369-26.442620.47071.2182
110.02360.0275-0.00090.0360.01280.05540.01780.0111-0.23610.1573-0.26670.01310.40390.3380.00080.18650.02310.03370.2662-0.01340.1878-12.7967-8.260916.032
120.1659-0.0101-0.12110.618-0.10120.1082-0.2734-0.02030.32460.037-0.0255-0.2392-0.34250.4626-0.07840.2531-0.0131-0.00490.29880.03520.2515-13.70623.57714.2673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 13 THROUGH 31 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 32 THROUGH 54 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 55 THROUGH 81 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 82 THROUGH 114 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 115 THROUGH 139 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 140 THROUGH 233 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 234 THROUGH 272 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 273 THROUGH 297 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 298 THROUGH 316 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 317 THROUGH 350 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 5 THROUGH 11 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 12 THROUGH 24 )

+
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