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- PDB-7ss1: The structure of NTMT1 in complex with compound GD433 -

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Basic information

Entry
Database: PDB / ID: 7ss1
TitleThe structure of NTMT1 in complex with compound GD433
ComponentsN-terminal Xaa-Pro-Lys N-methyltransferase 1
KeywordsTRANSFERASE/INHIBITOR / ntmt1 / methyltransferase / inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-AKF / S-ADENOSYL-L-HOMOCYSTEINE / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYadav, R. / Guangping, D. / Deng, Y. / Huang, R. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Discovery of a first-in-class small molecule inhibitor for Protein N-terminal methyltransferases 1/2
Authors: Yadav, R. / Guangping, D. / Deng, Y. / Huang, R. / Noinaj, N.
History
DepositionNov 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2206
Polymers54,6402
Non-polymers1,5804
Water0
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1103
Polymers27,3201
Non-polymers7902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1103
Polymers27,3201
Non-polymers7902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.909, 89.909, 141.542
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 5 and (name N...
21(chain B and (resid 4 through 38 or resid 40...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 4 through 5 and (name N...A4 - 5
121(chain A and ((resid 4 through 5 and (name N...A4 - 301
131(chain A and ((resid 4 through 5 and (name N...A4 - 301
141(chain A and ((resid 4 through 5 and (name N...A4 - 301
151(chain A and ((resid 4 through 5 and (name N...A4 - 301
211(chain B and (resid 4 through 38 or resid 40...B4 - 38
221(chain B and (resid 4 through 38 or resid 40...B40 - 100
231(chain B and (resid 4 through 38 or resid 40...B102 - 124
241(chain B and (resid 4 through 38 or resid 40...B126 - 177
251(chain B and (resid 4 through 38 or resid 40...B179 - 301
261(chain B and (resid 4 through 38 or resid 40...B401

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Components

#1: Protein N-terminal Xaa-Pro-Lys N-methyltransferase 1 / Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal ...Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal RCC1 methyltransferase / X-Pro-Lys N-terminal protein methyltransferase 1A / NTM1A


Mass: 27320.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-AKF / (1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluoro-3-hydroxyphenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate


Mass: 405.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24FN3O3S / Feature type: SUBJECT OF INVESTIGATION
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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES: NaOH (pH 9.5), 10% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25773 / % possible obs: 99.6 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.046 / Rrim(I) all: 0.138 / Χ2: 1.755 / Net I/σ(I): 5 / Num. measured all: 244434
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.49101.70425540.3050.5681.7971.402100
2.49-2.5910.31.70825930.4560.561.7991.299100
2.59-2.710.21.40225640.7330.4611.4761.236100
2.7-2.85101.02626090.9010.3411.0821.17100
2.85-3.029.30.68225770.9560.2350.7221.16199.9
3.02-3.269.70.38125610.9870.1280.4021.289100
3.26-3.5810.30.19725980.9940.0650.2081.775100
3.58-4.190.13825820.9940.0490.1472.53399.6
4.1-5.177.60.07925230.9970.0310.0863.40197.8
5.17-508.40.05526120.9990.020.0582.9998.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PVB

6pvb


Resolution: 2.4→42.85 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 45.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2992 1974 7.69 %
Rwork0.2482 23681 -
obs0.2519 25655 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.01 Å2 / Biso mean: 98.3947 Å2 / Biso min: 48.69 Å2
Refinement stepCycle: final / Resolution: 2.4→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 108 0 3607
Biso mean--107.48 --
Num. residues----441
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2015X-RAY DIFFRACTION18.052TORSIONAL
12B2015X-RAY DIFFRACTION18.052TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.440.61791320.6501155791
2.44-2.510.56091470.58341724100
2.51-2.580.51141410.53191689100
2.58-2.660.51921390.47851714100
2.66-2.760.47741380.4225168799
2.76-2.870.42081430.38451690100
2.87-30.40241500.346171699
3-3.160.3571380.3185167199
3.16-3.350.37531500.27851719100
3.35-3.610.31861430.25821701100
3.61-3.980.32041380.2378170799
3.98-4.550.24391390.1991169198
4.55-5.730.21291350.1894169098
5.73-42.850.2281410.1681172599

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