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- PDB-7szc: Crystal Structure Analysis of human PRPK complex with a compound -

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Basic information

Entry
Database: PDB / ID: 7szc
TitleCrystal Structure Analysis of human PRPK complex with a compound
Components
  • EKC/KEOPS complex subunit TP53RK
  • EKC/KEOPS complex subunit TPRKB
KeywordsTRANSFERASE / protein kinase / p53 / immunomodulatory drugs / IMiDs
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase ...tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / hydrolase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Lipopolysaccharide kinase (Kdo/WaaP) family / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-DO0 / D(-)-TARTARIC ACID / EKC/KEOPS complex subunit TP53RK / EKC/KEOPS complex subunit TPRKB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biorxiv / Year: 2021
Title: Development of PRPK Directed Phthalimides
Authors: Seo, H.-S. / Mizutani, T. / Hideshima, T. / Vangos, N.E. / Zhang, T. / Anderson, K.C. / Gray, N.S. / Dhe-Paganon, S.
History
DepositionNov 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EKC/KEOPS complex subunit TP53RK
B: EKC/KEOPS complex subunit TPRKB
C: EKC/KEOPS complex subunit TP53RK
D: EKC/KEOPS complex subunit TPRKB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5468
Polymers96,6704
Non-polymers8774
Water11,782654
1
A: EKC/KEOPS complex subunit TP53RK
B: EKC/KEOPS complex subunit TPRKB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7734
Polymers48,3352
Non-polymers4382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-16 kcal/mol
Surface area18050 Å2
MethodPISA
2
C: EKC/KEOPS complex subunit TP53RK
D: EKC/KEOPS complex subunit TPRKB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7734
Polymers48,3352
Non-polymers4382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-17 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.290, 48.240, 128.550
Angle α, β, γ (deg.)90.000, 96.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EKC/KEOPS complex subunit TP53RK / Atypical serine/threonine protein kinase TP53RK / Nori-2 / TP53-regulating kinase / p53-related protein kinase


Mass: 28358.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53RK, C20orf64, PRPK / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96S44, Hydrolases; Acting on acid anhydrides, non-specific serine/threonine protein kinase
#2: Protein EKC/KEOPS complex subunit TPRKB / PRPK-binding protein / TP53RK-binding protein


Mass: 19976.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPRKB, CGI-121, My019 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y3C4
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-DO0 / 4-hydroxy-2-[(3R)-3-methyl-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione


Mass: 288.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 200mM Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.71→63.92 Å / Num. obs: 96583 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.39 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.046 / Net I/σ(I): 15.7 / Num. measured all: 330553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.71-1.743.51.21695748100.6331.20999.9
4.64-63.963.251.61603449760.0120.02197.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ENP, 4WW5

3enp

4ww5


Resolution: 1.71→63.92 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 4858 5.03 %
Rwork0.1772 91701 -
obs0.1786 96559 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.64 Å2 / Biso mean: 37.0314 Å2 / Biso min: 17.76 Å2
Refinement stepCycle: final / Resolution: 1.71→63.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6099 0 86 654 6839
Biso mean--28.37 44.86 -
Num. residues----801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.730.43622070.415630343241100
1.73-1.750.42471610.392830043165100
1.75-1.770.37671760.350429993175100
1.77-1.790.3371500.316231143264100
1.79-1.820.32791650.290830063171100
1.82-1.840.31650.271830853250100
1.84-1.870.27061600.252830463206100
1.87-1.90.24971680.235230143182100
1.9-1.930.23721760.207630873263100
1.93-1.960.24721560.202230193175100
1.96-1.990.24361520.194230863238100
1.99-2.030.26571530.194930223175100
2.03-2.070.23681540.195930513205100
2.07-2.110.21921590.194330893248100
2.11-2.150.21711270.200430663193100
2.15-2.20.22481870.203730603247100
2.2-2.260.21141760.166229943170100
2.26-2.320.21271650.173930553220100
2.32-2.390.19211520.174830763228100
2.39-2.470.20971580.17023037319599
2.47-2.550.21881810.174530673248100
2.55-2.660.20611560.1773072322899
2.66-2.780.21791510.18263015316699
2.78-2.920.21931710.17573081325299
2.92-3.110.2211520.1713052320499
3.11-3.350.21421660.17353058322499
3.35-3.680.18671500.1533084323498
3.68-4.220.15281510.14023051320298
4.22-5.310.14091630.14433113327699
5.31-63.920.20461500.17663164331497
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)
11.27790.22480.24170.5717-0.56721.5687-0.2070.49410.3706-0.1059-0.0414-0.3309-0.92670.1749-0.01260.386-0.0930.00910.36490.06440.3257-9.673818.6008-52.3392
21.1162-0.32321.5360.9426-0.31091.9077-0.0214-0.05760.28430.00610.0024-0.2605-0.05870.192-00.3147-0.00230.01970.23450.01370.3151-8.470711.2474-40.3598
31.9667-0.42921.54261.0062-1.21751.8428-0.00430.4743-0.1441-0.3295-0.0803-0.09180.31940.27310.00350.33940.0191-0.00760.2544-0.01390.2751-11.5514-0.9107-47.0752
40.7907-0.06120.80471.4691-0.86641.26890.00020.03640.03670.05330.00080.0144-0.1328-0.13870.00010.2491-0.00230.02480.17950.01460.2366-17.35996.3938-39.9728
52.3646-0.6156-0.52223.117-1.03912.15210.019-0.54780.12040.5857-0.07860.0495-0.1158-0.19140.00060.3231-0.02970.02930.30010.01860.2814-13.9536-5.5177-21.1314
61.43930.11020.27752.0051-1.64961.93040.0501-0.1498-0.04130.08860.05890.1453-0.0546-0.1271-0.00070.234-0.01130.01250.20010.02020.2235-14.2126-3.7413-32.3384
70.7937-0.1040.29731.3048-0.59040.59750.07050.0332-0.1690.1264-0.0503-0.41790.26740.38560.00190.29860.0004-0.02220.25940.03110.3116-4.7331-12.1276-30.0596
81.8604-0.7067-1.29272.987-0.83161.4985-0.0062-0.1714-0.41950.15810.0236-0.18190.12740.1109-0.00010.2669-0.01350.02540.24970.1010.2699-11.9496-14.2074-22.4323
92.2152-0.10690.99651.42320.48161.26290.08350.5009-1.13470.0819-0.0798-0.6770.49020.4240.02850.40650.0194-0.04440.23180.02450.4047-4.6627-22.0878-31.0155
100.57430.61470.18170.71940.40520.5671-0.0139-0.09390.5869-0.0164-0.11550.1447-0.5835-0.0631-0.00130.43570.02570.00070.3009-0.00640.3976-27.245623.537-48.1561
111.5383-1.0272-0.53711.8816-0.62091.9581-0.01980.50560.4108-0.03860.01980.4769-0.1373-0.3205-0.00610.28080.0353-0.0270.42440.09340.3577-42.284718.4415-57.9577
123.0343-0.5665-0.59790.92830.27891.36560.04450.17610.2803-0.03350.07110.266-0.059-0.13790.00230.25440.00230.01250.22430.05010.2572-30.117813.9131-53.5684
130.30430.42040.08730.5368-0.04980.34450.11910.3401-0.1244-0.4525-0.0659-0.00780.12210.15560.00090.35120.03570.01550.34140.01330.2794-26.662310.4171-60.72
140.1909-0.3069-0.16950.49070.27950.27250.27680.6385-1.0222-0.4105-0.13740.72930.414-0.1680.00280.39650.03-0.08830.4161-0.11040.4599-32.90532.2333-57.9881
151.3405-1.3419-0.1741.30450.27931.7212-0.14720.3570.1705-0.14750.16040.6589-0.1542-0.49130.00050.3016-0.0055-0.02540.38930.04770.3724-40.239916.0265-56.1558
160.29180.2824-0.43280.8736-0.70570.70130.05660.52110.0244-0.83960.2360.0082-0.3771-0.0802-0.0150.4207-0.00340.01750.33440.04590.4449-37.862528.5086-59.0431
171.05730.0474-0.09320.5139-0.14270.51390.0025-0.33270.20230.31120.36961.0396-0.132-0.75010.01660.3680.08690.09450.50230.07910.5381-45.556317.1775-46.8815
183.53631.0779-0.4432.4624-1.47420.9019-0.19390.9485-0.7752-0.6290.76191.33850.3969-0.5660.23880.2866-0.04660.0030.41910.15940.5725-39.36270.3201-46.3047
193.7206-0.03443.8650.35960.55295.10290.169-0.5088-1.43070.03770.66790.38681.382-1.4390.35250.5187-0.18930.01790.62410.20510.6325-31.7727-3.2767-38.1472
201.31670.16910.82361.0562-0.54371.12140.0623-0.0981-0.3698-0.1679-0.01120.19110.13780.00880.00060.30380.01010.00350.25610.02250.3288-26.02492.6312-46.6573
210.6954-0.3498-0.15231.0546-1.2962.07510.1016-0.5961-0.68710.8290.11160.1574-0.1389-0.59210.04580.4232-0.05650.04560.64040.18350.5155-60.509-22.5361-6.7862
220.8154-0.6850.21811.2860.47120.5611-0.0236-0.4042-0.06140.19530.10310.18370.0106-0.14910.00030.340.0011-0.01230.43580.0130.2981-60.7208-7.6883-13.9519
230.8324-0.65720.16670.4403-0.06240.7436-0.1406-0.3652-0.45570.01850.11480.0346-0.0274-0.1976-0.00030.3347-0.0318-0.00950.41430.06870.3353-63.3518-14.6838-16.4543
241.5725-1.46010.8261.6018-1.07271.4490.10150.1547-0.228-0.18130.21250.27180.4081-0.16110.00440.3322-0.0076-0.06230.340.02660.341-58.6498-19.2443-26.1786
251.5339-0.88470.94531.7008-0.72141.30780.0149-0.2119-0.10430.28230.0266-0.121-0.1199-0.1282-0.00030.2655-0.0315-0.02180.32750.03960.2746-52.7834-11.1592-19.9403
262.43761.18810.89491.8592-0.4953.48410.01980.13560.57350.1140.0199-0.2539-0.48840.1445-0.00070.2769-0.01570.01760.33250.0580.3291-55.03883.6402-34.9169
271.9706-0.39830.49681.2183-1.64252.39690.06580.05510.14630.1487-0.0896-0.12520.09040.1185-0.00020.23750.00870.01930.28770.02680.2864-55.9032-4.9196-31.039
281.2119-0.0448-0.07160.9186-1.14171.46430.16590.3356-0.0042-0.3203-0.20210.2689-0.2004-0.1948-0.00040.24340.0189-0.00690.33340.03590.2873-65.4446-3.6629-39.6547
291.70561.0950.11661.1639-0.66671.7170.20210.64030.4616-0.1879-0.1361-0.163-0.251-0.0331-0.00040.286-0.0030.01120.41740.1080.3187-58.57913.8851-42.4336
300.8487-1.06820.3041.3125-0.40610.29370.04150.3443-0.6713-0.38830.07080.51960.4107-0.28960.00370.40070.0907-0.03240.4487-0.00830.2226-65.6701-5.621-49.0221
311.3099-0.8071-0.58811.24070.60071.159-0.3981-1.17270.33360.51890.3786-0.2756-0.70660.0516-0.00720.48560.0361-0.04530.60160.03870.3927-42.0829-17.3649-2.3492
320.6563-0.79050.02782.2815-1.23612.3080.16060.17630.0838-0.3039-0.258-0.41370.17180.4371-0.00050.27550.02140.00340.52050.06370.2884-28.4672-28.1662-6.2887
331.20110.63140.96020.82570.29910.66570.1584-0.1739-0.00250.3775-0.2327-0.2138-0.18130.222300.30620.01440.02120.4950.05860.3596-32.1126-25.3031-11.0642
341.6547-1.03330.7480.8494-0.2491.3471-0.0041-0.0723-0.6864-0.09760.1730.12180.5017-0.0294-0.00020.3087-0.0135-0.02290.30360.08090.3965-44.8562-26.9518-12.3929
352.1165-1.46021.54112.3787-0.54881.46290.23050.1529-0.3927-0.2593-0.1544-0.08960.35730.3702-0.00060.32510.04630.00760.40160.02330.3129-34.0608-28.0699-14.3237
360.272-0.03440.12990.5539-0.38630.628-0.2428-0.8001-0.54630.09660.11810.7532-0.0396-0.23960.00040.45030.0533-0.04960.71730.05150.4546-31.8088-27.89383.9399
371.0465-0.1899-0.15520.13-0.26510.8607-0.01770.28950.61170.3991-0.4661-0.7636-0.52461.4758-0.00030.427-0.0744-0.0910.64810.08250.5249-24.3835-17.7416-9.1795
382.37730.0699-3.92070.0012-0.10156.4513-0.43620.4095-1.2545-0.2328-0.3156-0.50221.30161.366-0.3720.26250.12220.04690.59070.1860.376-31.0731-18.9941-25.683
392.1643-0.82930.66622.28520.06910.27160.26070.75670.8047-1.0578-0.7288-1.32050.6481.0266-0.0840.50320.05850.11480.63860.14080.5291-38.1192-10.778-29.9046
400.821-0.0497-0.25420.3273-0.29420.9837-0.05020.30350.0981-0.18270.07140.04260.02110.15420.00040.27660.0013-0.01570.36470.00360.2952-44.2135-18.5036-23.0125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 35 )A18 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 69 )A36 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 93 )A70 - 93
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 121 )A94 - 121
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 156 )A122 - 156
6X-RAY DIFFRACTION6chain 'A' and (resid 157 through 192 )A157 - 192
7X-RAY DIFFRACTION7chain 'A' and (resid 193 through 210 )A193 - 210
8X-RAY DIFFRACTION8chain 'A' and (resid 211 through 231 )A211 - 231
9X-RAY DIFFRACTION9chain 'A' and (resid 232 through 246 )A232 - 246
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 13 )B0 - 13
11X-RAY DIFFRACTION11chain 'B' and (resid 14 through 35 )B14 - 35
12X-RAY DIFFRACTION12chain 'B' and (resid 36 through 67 )B36 - 67
13X-RAY DIFFRACTION13chain 'B' and (resid 68 through 83 )B68 - 83
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 96 )B84 - 96
15X-RAY DIFFRACTION15chain 'B' and (resid 97 through 111 )B97 - 111
16X-RAY DIFFRACTION16chain 'B' and (resid 112 through 125 )B112 - 125
17X-RAY DIFFRACTION17chain 'B' and (resid 126 through 141 )B126 - 141
18X-RAY DIFFRACTION18chain 'B' and (resid 142 through 149 )B142 - 149
19X-RAY DIFFRACTION19chain 'B' and (resid 150 through 160 )B150 - 160
20X-RAY DIFFRACTION20chain 'B' and (resid 161 through 175 )B161 - 175
21X-RAY DIFFRACTION21chain 'C' and (resid 18 through 35 )C18 - 35
22X-RAY DIFFRACTION22chain 'C' and (resid 36 through 52 )C36 - 52
23X-RAY DIFFRACTION23chain 'C' and (resid 53 through 69 )C53 - 69
24X-RAY DIFFRACTION24chain 'C' and (resid 70 through 93 )C70 - 93
25X-RAY DIFFRACTION25chain 'C' and (resid 94 through 121 )C94 - 121
26X-RAY DIFFRACTION26chain 'C' and (resid 122 through 156 )C122 - 156
27X-RAY DIFFRACTION27chain 'C' and (resid 157 through 192 )C157 - 192
28X-RAY DIFFRACTION28chain 'C' and (resid 193 through 210 )C193 - 210
29X-RAY DIFFRACTION29chain 'C' and (resid 211 through 231 )C211 - 231
30X-RAY DIFFRACTION30chain 'C' and (resid 232 through 246 )C232 - 246
31X-RAY DIFFRACTION31chain 'D' and (resid 0 through 12 )D0 - 12
32X-RAY DIFFRACTION32chain 'D' and (resid 13 through 35 )D13 - 35
33X-RAY DIFFRACTION33chain 'D' and (resid 36 through 50 )D36 - 50
34X-RAY DIFFRACTION34chain 'D' and (resid 51 through 83 )D51 - 83
35X-RAY DIFFRACTION35chain 'D' and (resid 84 through 112 )D84 - 112
36X-RAY DIFFRACTION36chain 'D' and (resid 113 through 125 )D113 - 125
37X-RAY DIFFRACTION37chain 'D' and (resid 126 through 141 )D126 - 141
38X-RAY DIFFRACTION38chain 'D' and (resid 142 through 149 )D142 - 149
39X-RAY DIFFRACTION39chain 'D' and (resid 150 through 160 )D150 - 160
40X-RAY DIFFRACTION40chain 'D' and (resid 161 through 175 )D161 - 175

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