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- PDB-7k3d: The structure of NTMT1 in complex with compound DC1-13 -

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Basic information

Entry
Database: PDB / ID: 7k3d
TitleThe structure of NTMT1 in complex with compound DC1-13
ComponentsN-terminal Xaa-Pro-Lys N-methyltransferase 1
Keywordstransferase/transferase inhibitor / methyltransferase / enzyme / inhibitor complex / TRANSFERASE / 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 / cytoplasm / cytosol
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Chem-VWP / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsChen, D. / Huang, R. / Noinaj, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA023168 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Structure-based Discovery of Cell-Potent Peptidomimetic Inhibitors for Protein N-Terminal Methyltransferase 1.
Authors: Chen, D. / Dong, G. / Deng, Y. / Noinaj, N. / Huang, R.
History
DepositionSep 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,5386
Polymers54,6402
Non-polymers1,8984
Water3,711206
1
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2693
Polymers27,3201
Non-polymers9492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2693
Polymers27,3201
Non-polymers9492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.860, 81.662, 84.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 38 or resid 40...
21(chain B and (resid 3 through 6 or (resid 7...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain A and (resid 3 through 38 or resid 40...AB3 - 3821 - 56
12ILEILETHRTHR(chain A and (resid 3 through 38 or resid 40...AB40 - 6258 - 80
13CYSCYSPHEPHE(chain A and (resid 3 through 38 or resid 40...AB64 - 8482 - 102
14ARGARGARGARG(chain A and (resid 3 through 38 or resid 40...AB85103
15SERSERARGARG(chain A and (resid 3 through 38 or resid 40...AB3 - 22321 - 241
16SERSERARGARG(chain A and (resid 3 through 38 or resid 40...AB3 - 22321 - 241
17SERSERARGARG(chain A and (resid 3 through 38 or resid 40...AB3 - 22321 - 241
18SERSERARGARG(chain A and (resid 3 through 38 or resid 40...AB3 - 22321 - 241
19SERSERARGARG(chain A and (resid 3 through 38 or resid 40...AB3 - 22321 - 241
21SERSERILEILE(chain B and (resid 3 through 6 or (resid 7...BA3 - 621 - 24
22GLUGLUGLUGLU(chain B and (resid 3 through 6 or (resid 7...BA725
23SERSERARGARG(chain B and (resid 3 through 6 or (resid 7...BA3 - 22321 - 241
24SERSERARGARG(chain B and (resid 3 through 6 or (resid 7...BA3 - 22321 - 241
25SERSERARGARG(chain B and (resid 3 through 6 or (resid 7...BA3 - 22321 - 241

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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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VWP / N~2~-{(2S)-1-[(naphthalen-1-yl)acetyl]-2,5-dihydro-1H-pyrrole-2-carbonyl}-L-lysyl-L-argininamide


Mass: 564.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H40N8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.5 M Ammonium sulfate; 0.1 M MES pH 6.5

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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 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 19735 / % possible obs: 88.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.128 / Rrim(I) all: 0.271 / Χ2: 1.524 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.433.60.89420010.5180.481.021.04692
2.43-2.533.60.7720540.590.4170.8811.07293
2.53-2.653.70.62820580.6910.3310.7141.09592.4
2.65-2.793.90.52519920.7720.2690.5931.21691.3
2.79-2.963.90.39419750.8560.2040.4461.36889.4
2.96-3.193.70.28919530.9270.1560.331.63187.6
3.19-3.513.40.18218990.9520.1030.211.93985.3
3.51-4.023.40.12318850.9780.0690.1421.90683.5
4.02-5.063.50.08419160.990.0480.0971.94884
5.06-503.30.07620020.9930.0450.0892.34383.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTN

6dtn


Resolution: 2.34→42.17 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1973 10.02 %
Rwork0.2054 17727 -
obs0.2107 19700 88.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.25 Å2 / Biso mean: 26.2111 Å2 / Biso min: 11.16 Å2
Refinement stepCycle: final / Resolution: 2.34→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 134 209 3855
Biso mean--26.81 29.76 -
Num. residues----442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2022X-RAY DIFFRACTION10.789TORSIONAL
12B2022X-RAY DIFFRACTION10.789TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.34-2.40.28531440.2364128690
2.4-2.470.3291410.2319129993
2.47-2.540.32441520.2372130793
2.54-2.620.27461460.2302131693
2.62-2.710.29621300.2245130591
2.71-2.820.30981570.2233126890
2.82-2.950.29681490.2249126390
2.95-3.110.2791430.226125988
3.11-3.30.27081250.2135122985
3.3-3.560.25781480.201122985
3.56-3.910.2461320.1736120083
3.91-4.480.1589130121784
4.48-5.640.22251390.1702126585
5.64-42.170.26731370.2249128482

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