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- PDB-6pvb: The structure of NTMT1 in complex with compound 6 -

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Basic information

Entry
Database: PDB / ID: 6pvb
TitleThe structure of NTMT1 in complex with compound 6
Components
  • AMINO GROUP-()-(2~{S})-2-azanylpropanal-()-ISOLEUCINE-()-ARGININE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine
  • N-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-proline dimethylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-proline dimethylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / 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 / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNoinaj, N. / Chen, D. / Huang, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1U01CA214649-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM117275-01A1 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Probing the Plasticity in the Active Site of Protein N-terminal Methyltransferase 1 Using Bisubstrate Analogues.
Authors: Chen, D. / Dong, C. / Dong, G. / Srinivasan, K. / Min, J. / Noinaj, N. / Huang, R.
History
DepositionJul 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
A: AMINO GROUP-()-(2~{S})-2-azanylpropanal-()-ISOLEUCINE-()-ARGININE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7493
Polymers28,3642
Non-polymers3841
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-5 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.947, 72.947, 82.089
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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.: 1
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: Protein/peptide AMINO GROUP-()-(2~{S})-2-azanylpropanal-()-ISOLEUCINE-()-ARGININE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine


Mass: 1044.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M lithium sulfate, 0.1 M sodium HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 41225 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 1 / Rsym value: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2962 / CC1/2: 0.17 / Rsym value: 3.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTN

6dtn


Resolution: 1.5→29.48 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1997 4.86 %
Rwork0.2048 39067 -
obs0.2057 41064 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.95 Å2 / Biso mean: 38.2219 Å2 / Biso min: 20.04 Å2
Refinement stepCycle: final / Resolution: 1.5→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 102 164 2039
Biso mean--49.1 43.43 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.38941330.36242599273294
1.53-1.570.33511420.333127502892100
1.57-1.620.33411430.336927962939100
1.62-1.670.38631410.306327422883100
1.67-1.730.38531440.314727972941100
1.73-1.80.28231410.277827582899100
1.8-1.880.26141400.256727942934100
1.88-1.980.26541430.222327752918100
1.98-2.110.25731420.223428062948100
2.11-2.270.24291400.198928082948100
2.27-2.50.23951480.224828112959100
2.5-2.860.24571400.203928112951100
2.86-3.60.20881490.193628563005100
3.61-29.480.17111510.165229643115100

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