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- PDB-7sok: Structure of Nicotinamide N-Methyltransferase (NNMT) in complex w... -

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Basic information

Entry
Database: PDB / ID: 7sok
TitleStructure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor II329
ComponentsNNMT protein
KeywordsTRANSFERASE/INHIBITOR / NNMT1 / inhibitor / methylation / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


nicotinamide metabolic process / nicotinamide N-methyltransferase activity / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / response to organonitrogen compound / methylation / response to xenobiotic stimulus / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-9XL / DI(HYDROXYETHYL)ETHER / NNMT protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsYadav, R. / Iyamu, I.D. / Huang, R. / Noinaj, N.
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: To Be Published
Title: Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor II329
Authors: Iyamu, I. / Vilseck, J.Z. / Yadav, R. / Noinaj, N. / Huang, R.
History
DepositionOct 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
C: NNMT protein
A: NNMT protein
B: NNMT protein
D: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,87716
Polymers125,8644
Non-polymers3,01312
Water5,891327
1
C: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5387
Polymers31,4661
Non-polymers1,0726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2194
Polymers31,4661
Non-polymers7533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1133
Polymers31,4661
Non-polymers6472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0072
Polymers31,4661
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.821, 62.596, 79.781
Angle α, β, γ (deg.)110.070, 103.820, 103.850
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 8 or (resid 9...
21(chain B and (resid 5 through 12 or (resid 13...
31(chain C and (resid 5 through 8 or (resid 9...
41(chain D and (resid 5 through 8 or (resid 9...

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
11PHEPHELYSLYS(chain A and (resid 5 through 8 or (resid 9...AB5 - 824 - 27
12ASPASPASPASP(chain A and (resid 5 through 8 or (resid 9...AB928
13GLYGLYLEULEU(chain A and (resid 5 through 8 or (resid 9...AB4 - 26023 - 279
21PHEPHELEULEU(chain B and (resid 5 through 12 or (resid 13...BC5 - 1224 - 31
22SERSERSERSER(chain B and (resid 5 through 12 or (resid 13...BC1332
23PHEPHELEULEU(chain B and (resid 5 through 12 or (resid 13...BC5 - 26024 - 279
31PHEPHELYSLYS(chain C and (resid 5 through 8 or (resid 9...CA5 - 824 - 27
32ASPASPASPASP(chain C and (resid 5 through 8 or (resid 9...CA928
33GLYGLYLEULEU(chain C and (resid 5 through 8 or (resid 9...CA-6 - 26013 - 279
34GLYGLYLEULEU(chain C and (resid 5 through 8 or (resid 9...CA-6 - 26013 - 279
35GLYGLYLEULEU(chain C and (resid 5 through 8 or (resid 9...CA-6 - 26013 - 279
36GLYGLYLEULEU(chain C and (resid 5 through 8 or (resid 9...CA-6 - 26013 - 279
41PHEPHELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD5 - 824 - 27
42ASPASPASPASP(chain D and (resid 5 through 8 or (resid 9...DD928
43PHEPHELEULEU(chain D and (resid 5 through 8 or (resid 9...DD5 - 26024 - 279

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Components

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


Mass: 31466.033 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-9XL / (2S)-2-amino-4-([3-(3-carbamoylphenyl)prop-2-yn-1-yl]{[(1R,2R,3S,4R)-4-(4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,3-dihydroxycyclopentyl]methyl}amino)butanoic acid


Mass: 540.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H29ClN6O5
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris:HCl, pH 5.5, 25% w/v PEG3350

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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: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 59068 / % possible obs: 91 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.092 / Rrim(I) all: 0.177 / Χ2: 1.261 / Net I/σ(I): 5.2 / Num. measured all: 213163
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.153.40.75654570.5830.4780.8971.02384.6
2.15-2.243.50.64860110.6560.4050.766192.4
2.24-2.343.60.53559290.7470.3290.6291.03392
2.34-2.473.60.44259320.8110.2690.5181.03491.1
2.47-2.623.60.3556760.8620.2150.4121.08387.5
2.62-2.823.60.2758730.9170.1640.3161.15589.7
2.82-3.113.70.18961240.960.1140.2211.28994.6
3.11-3.563.70.11260380.9850.0670.131.45593
3.56-4.483.70.06759190.9930.040.0781.66590.9
4.48-503.80.05661090.9960.0330.0651.73394.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6PVS

6pvs


Resolution: 2.08→41.14 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 2012 3.72 %
Rwork0.2069 52098 -
obs0.2083 54110 89.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.15 Å2 / Biso mean: 29.1324 Å2 / Biso min: 11.44 Å2
Refinement stepCycle: final / Resolution: 2.08→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8003 0 220 327 8550
Biso mean--32.53 31.56 -
Num. residues----1036
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4487X-RAY DIFFRACTION10.674TORSIONAL
12B4487X-RAY DIFFRACTION10.674TORSIONAL
13C4487X-RAY DIFFRACTION10.674TORSIONAL
14D4487X-RAY DIFFRACTION10.674TORSIONAL
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 (%)
2.08-2.130.36851220.32143225334777
2.13-2.190.36691260.30133770389690
2.19-2.250.30061580.27693771392991
2.25-2.320.32761360.27353776391290
2.32-2.410.33331320.25943731386390
2.41-2.50.31361530.25073695384889
2.5-2.620.27521510.24413465361684
2.62-2.760.27471410.23323603374486
2.76-2.930.28791490.2263884403393
2.93-3.150.25211480.21673883403194
3.16-3.470.22251550.20013877403293
3.47-3.970.22441310.16723561369286
3.97-5.010.16831610.15144000416196
5.01-41.140.18031490.15643857400693

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