[English] 日本語
Yorodumi
- PDB-12oc: Crystal Structure of serine/threonine-protein kinase (AEK1) from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 12oc
TitleCrystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with ATP
ComponentsPutative rac serine-threonine kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / serine/threonine-protein kinase
Function / homology
Function and homology information


protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/Threonine Kinase AGC, catalytic domain / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Serine/threonine protein kinase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with ATP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative rac serine-threonine kinase
B: Putative rac serine-threonine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4734
Polymers83,4592
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-36 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.260, 85.260, 192.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Putative rac serine-threonine kinase


Mass: 41729.266 Da / Num. of mol.: 2 / Fragment: residues 123-474 / Mutation: T185I, V227F, N314S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_45g89 / Plasmid: TrcrB.01480.a.WW4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4E2L0
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM ATP solubilized in 3.0M Malonate, ...Details: 3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM ATP solubilized in 3.0M Malonate, pH 5.0 (cryo solution) which displaced the ATP. plate Liu-S-198, Puck: PSL-0203, Cryo: 3.0M Sodium Malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 30, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.68→48.45 Å / Num. obs: 17774 / % possible obs: 94.9 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.049 / Rrim(I) all: 0.163 / Net I/σ(I): 16.4
Reflection shellResolution: 2.68→2.857 Å / Redundancy: 21.5 % / Rmerge(I) obs: 1.737 / Num. unique obs: 889 / CC1/2: 0.75 / Rpim(I) all: 0.53 / Rrim(I) all: 1.816 / % possible all: 87.9

-
Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→48.45 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 897 5.05 %
Rwork0.233 --
obs0.2354 17764 75.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 62 0 5143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025275
X-RAY DIFFRACTIONf_angle_d0.557176
X-RAY DIFFRACTIONf_dihedral_angle_d12.9231938
X-RAY DIFFRACTIONf_chiral_restr0.048778
X-RAY DIFFRACTIONf_plane_restr0.004906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.850.4118400.3444795X-RAY DIFFRACTION22
2.85-3.070.3864590.29451420X-RAY DIFFRACTION39
3.07-3.380.32592020.30263320X-RAY DIFFRACTION91
3.38-3.860.29751730.24743706X-RAY DIFFRACTION100
3.87-4.870.24391920.20173735X-RAY DIFFRACTION100
4.87-48.450.27142310.2133891X-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)
10.3292-0.1631-0.30570.08210.15150.2873-0.0819-0.2739-0.00930.0574-0.13620.05520.0710.4061-0.04520.3525-0.1412-0.10960.36550.10520.388933.5472-40.65862.8384
20.07370.0952-0.04230.1117-0.06870.04450.0432-0.19590.09770.3057-0.06410.2642-0.30790.1869-0.0380.5107-0.13110.00760.25680.00860.29124.3456-28.4514-2.6068
30.0026-0.0105-0.00080.125-0.08910.0862-0.0199-0.0304-0.04470.12250.06370.09130.00320.00410.20160.4721-0.3352-0.07170.31540.17560.499619.6477-37.90252.5698
40.20250.0669-0.01650.0255-0.00450.00390.26-0.0477-0.06490.12170.16590.1764-0.1088-0.23390.74180.7461-0.11790.24620.16370.0950.498110.6395-29.44627.2661
50.00460.0099-0.01230.0393-0.03110.02710.03190.11050.07430.08590.0377-0.02-0.2031-0.06620.00310.8352-0.05250.21970.2832-0.01610.483817.444-15.7462-1.241
60.06660.03090.0430.1842-0.02190.11010.16020.1955-0.22870.11820.11810.3902-0.2332-0.59890.04750.43240.08270.21340.68470.29260.77153.3028-25.372-3.9533
70.02940.0419-0.02750.0529-0.0320.03570.0897-0.00260.19650.21490.49830.6327-0.3272-0.53640.23790.63810.01240.32240.83260.43331.0877-5.7348-28.89930.1477
80.2478-0.02030.1390.02130.01450.12970.2893-0.11270.13740.07030.14050.1954-0.2236-0.32981.21090.7860.00030.32440.32270.2430.40129.0125-33.406818.4628
90.32210.13510.0080.134-0.02160.5532-0.01710.0182-0.0607-0.39070.06970.05480.0660.082-0.08371.1923-0.5172-0.06090.6765-0.01020.69113.7023-48.0874-2.8108
100.22190.0448-0.21350.0867-0.22040.6431-0.10730.2642-0.379-0.64570.0329-0.0061.3089-0.2616-0.32491.593-0.280.06950.2629-0.23650.376518.3969-35.2323-30.8607
110.7285-0.264-0.20340.1498-0.07240.45640.06430.1733-0.1847-0.02880.08020.11110.2789-0.28680.24910.4386-0.09560.07010.20420.09870.292315.4466-18.8041-26.2503
120.9461-0.2009-0.32110.5004-0.36750.5152-0.00580.55730.1694-0.3653-0.089-0.12770.1099-0.0377-0.35270.6073-0.12780.05770.29130.15710.22126.9239-14.9244-34.3003
130.2023-0.14340.06120.0906-0.04290.02130.16830.0450.19560.1186-0.4245-0.15120.10210.0072-0.05070.5716-0.15410.05380.51460.08470.374534.3372-31.4674-20.4874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 125 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 192 )
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 228 )
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 271 )
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 293 )
6X-RAY DIFFRACTION6chain 'A' and (resid 294 through 334 )
7X-RAY DIFFRACTION7chain 'A' and (resid 335 through 391 )
8X-RAY DIFFRACTION8chain 'A' and (resid 392 through 418 )
9X-RAY DIFFRACTION9chain 'A' and (resid 419 through 466 )
10X-RAY DIFFRACTION10chain 'B' and (resid 125 through 268 )
11X-RAY DIFFRACTION11chain 'B' and (resid 269 through 334 )
12X-RAY DIFFRACTION12chain 'B' and (resid 335 through 418 )
13X-RAY DIFFRACTION13chain 'B' and (resid 419 through 467 )

+
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