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- PDB-6pvs: Structure of Nicotinamide N-Methyltransferase (NNMT) in complex w... -

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Basic information

Entry
Database: PDB / ID: 6pvs
TitleStructure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor LL320
ComponentsNNMT protein
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / Methyltransferase / Inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / Methylation / : / positive regulation of gluconeogenesis / methylation / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-P0V / Nicotinamide N-methyltransferase / NNMT protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.575 Å
AuthorsNoinaj, N. / Huang, R. / Chen, D. / Yadav, R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI127793 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM117275 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA214649-01 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Novel Propargyl-Linked Bisubstrate Analogues as Tight-Binding Inhibitors for NicotinamideN-Methyltransferase.
Authors: Chen, D. / Li, L. / Diaz, K. / Iyamu, I.D. / Yadav, R. / Noinaj, N. / Huang, R.
History
DepositionJul 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: NNMT protein
B: NNMT protein
C: NNMT protein
D: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9628
Polymers125,8644
Non-polymers2,0984
Water1,910106
1
A: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9912
Polymers31,4661
Non-polymers5251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9912
Polymers31,4661
Non-polymers5251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9912
Polymers31,4661
Non-polymers5251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9912
Polymers31,4661
Non-polymers5251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.230, 62.530, 108.359
Angle α, β, γ (deg.)82.720, 82.480, 68.340
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 29 or (resid 30...
21(chain B and (resid 4 through 98 or (resid 99...
31(chain C and (resid 4 through 29 or (resid 30...
41(chain D and (resid 4 through 29 or (resid 30...

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
11GLYGLYSERSER(chain A and (resid 4 through 29 or (resid 30...AA4 - 2923 - 48
12ARGARGARGARG(chain A and (resid 4 through 29 or (resid 30...AA3049
13HISHISLEULEU(chain A and (resid 4 through 29 or (resid 30...AA-9 - 26010 - 279
14HISHISLEULEU(chain A and (resid 4 through 29 or (resid 30...AA-9 - 26010 - 279
15HISHISLEULEU(chain A and (resid 4 through 29 or (resid 30...AA-9 - 26010 - 279
16HISHISLEULEU(chain A and (resid 4 through 29 or (resid 30...AA-9 - 26010 - 279
21GLYGLYLEULEU(chain B and (resid 4 through 98 or (resid 99...BB4 - 9823 - 117
22LYSLYSALAALA(chain B and (resid 4 through 98 or (resid 99...BB99 - 101118 - 120
23HISHISLEULEU(chain B and (resid 4 through 98 or (resid 99...BB-9 - 26010 - 279
24HISHISLEULEU(chain B and (resid 4 through 98 or (resid 99...BB-9 - 26010 - 279
25HISHISLEULEU(chain B and (resid 4 through 98 or (resid 99...BB-9 - 26010 - 279
26HISHISLEULEU(chain B and (resid 4 through 98 or (resid 99...BB-9 - 26010 - 279
31GLYGLYSERSER(chain C and (resid 4 through 29 or (resid 30...CC4 - 2923 - 48
32ARGARGARGARG(chain C and (resid 4 through 29 or (resid 30...CC3049
33GLYGLYLEULEU(chain C and (resid 4 through 29 or (resid 30...CC4 - 26023 - 279
34GLYGLYLEULEU(chain C and (resid 4 through 29 or (resid 30...CC4 - 26023 - 279
35GLYGLYLEULEU(chain C and (resid 4 through 29 or (resid 30...CC4 - 26023 - 279
41GLYGLYSERSER(chain D and (resid 4 through 29 or (resid 30...DD4 - 2923 - 48
42ARGARGARGARG(chain D and (resid 4 through 29 or (resid 30...DD3049
43SERSERLEULEU(chain D and (resid 4 through 29 or (resid 30...DD3 - 26022 - 279
44SERSERLEULEU(chain D and (resid 4 through 29 or (resid 30...DD3 - 26022 - 279
45SERSERLEULEU(chain D and (resid 4 through 29 or (resid 30...DD3 - 26022 - 279
46SERSERLEULEU(chain D and (resid 4 through 29 or (resid 30...DD3 - 26022 - 279

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Components

#1: Protein
NNMT protein / Nicotinamide N-methyltransferase / isoform CRA_a


Mass: 31466.033 Da / Num. of mol.: 4 / Mutation: K100A, E101A, E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT, hCG_39357 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FH49, UniProt: P40261*PLUS
#2: Chemical
ChemComp-P0V / 9-(5-{[(3R)-3-amino-3-carboxypropyl][3-(3-carbamoylphenyl)prop-2-yn-1-yl]amino}-5-deoxy-alpha-D-lyxofuranosyl)-9H-purin-6-amine


Mass: 524.529 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H28N8O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M bicine, pH 9.0, and 1.6 M ammonium sulfate

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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 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→52.85 Å / Num. obs: 31186 / % possible obs: 88.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 42.12 Å2 / CC1/2: 0.98 / Rsym value: 0.16 / Net I/σ(I): 1.9
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4912 / CC1/2: 0.4 / Rsym value: 1 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.575→52.845 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.3
RfactorNum. reflection% reflection
Rfree0.2921 3247 6.31 %
Rwork0.2326 --
obs0.2365 31186 72.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.37 Å2 / Biso mean: 44.6176 Å2 / Biso min: 21 Å2
Refinement stepCycle: final / Resolution: 2.575→52.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8144 0 260 106 8510
Biso mean--44.05 40.7 -
Num. residues----1055
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4875X-RAY DIFFRACTION14.817TORSIONAL
12B4875X-RAY DIFFRACTION14.817TORSIONAL
13C4875X-RAY DIFFRACTION14.817TORSIONAL
14D4875X-RAY DIFFRACTION14.817TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.575-2.61310.32531100.3266199470
2.6131-2.6540.37531690.3052206974
2.654-2.69750.33761350.3036214673
2.6975-2.7440.32911530.2943215175
2.744-2.79390.38421480.3075207575
2.7939-2.84760.36161560.2934228377
2.8476-2.90570.34071500.3067220478
2.9057-2.96890.34771400.2848220576
2.9689-3.0380.40141460.2772211375
3.038-3.11390.32831400.285206671
3.1139-3.19810.32511400.2759218178
3.1981-3.29220.35061670.2615227477
3.2922-3.39850.32851260.2603195471
3.3985-3.51990.33391580.2271221775
3.5199-3.66080.3063900.2301151669
3.6608-3.82740.26231040.2123167877
3.8274-4.02910.24131490.2126219077
4.0291-4.28140.27261480.1997220676
4.2814-4.61180.23091590.1799211474
4.6118-5.07560.23731430.1897209473
5.0756-5.80920.24861230.2013209972
5.8092-7.31590.3151320.2219214275
7.3159-52.8450.22861610.1787226578

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