[English] 日本語
Yorodumi
- PDB-5yjf: Co-crystal structure of Human Nicotinamide N-methyltransferase (N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yjf
TitleCo-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with small molecule analog of Nicotinamide
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT / NA / MNA / T2D
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
6-methoxy-1-methyl-2H-pyridine-3-carboxamide / S-ADENOSYL-L-HOMOCYSTEINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSwaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Hallur, M.S. / Rajagopal, S. / Ruf, S. / Dhakshinamoorthy, S. / Kannt, A. / Gosu, R.
CitationJournal: Sci Rep / Year: 2018
Title: A small molecule inhibitor of Nicotinamide N-methyltransferase for the treatment of metabolic disorders.
Authors: Kannt, A. / Rajagopal, S. / Kadnur, S.V. / Suresh, J. / Bhamidipati, R.K. / Swaminathan, S. / Hallur, M.S. / Kristam, R. / Elvert, R. / Czech, J. / Pfenninger, A. / Rudolph, C. / Schreuder, ...Authors: Kannt, A. / Rajagopal, S. / Kadnur, S.V. / Suresh, J. / Bhamidipati, R.K. / Swaminathan, S. / Hallur, M.S. / Kristam, R. / Elvert, R. / Czech, J. / Pfenninger, A. / Rudolph, C. / Schreuder, H. / Chandrasekar, D.V. / Mane, V.S. / Birudukota, S. / Shaik, S. / Zope, B.R. / Burri, R.R. / Anand, N.N. / Thakur, M.K. / Singh, M. / Parveen, R. / Kandan, S. / Mullangi, R. / Yura, T. / Gosu, R. / Ruf, S. / Dhakshinamoorthy, S.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
B: Nicotinamide N-methyltransferase
C: Nicotinamide N-methyltransferase
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,62712
Polymers126,4174
Non-polymers2,2108
Water1,27971
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.323, 132.976, 61.317
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Nicotinamide N-methyltransferase


Mass: 31604.184 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-8WO / 6-methoxy-1-methyl-2H-pyridine-3-carboxamide


Mass: 168.193 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2M Sodium chloride, 0.1M BIS-TRIS pH 5.8, 25 %(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.48→47.78 Å / Num. obs: 31948 / % possible obs: 96.4 % / Redundancy: 6.4 % / Net I/σ(I): 5.7
Reflection shellHighest resolution: 2.48 Å / Rmerge(I) obs: 0.885 / Rpim(I) all: 0.411

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ROD

3rod


Resolution: 2.49→47.78 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / SU B: 29.043 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28553 1617 5.1 %RANDOM
Rwork0.22374 ---
obs0.22693 30164 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.075 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å2-0.38 Å2
2--1.45 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.49→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7873 0 152 71 8096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228217
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2942.00511161
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1551019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71824.811318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.984151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271525
X-RAY DIFFRACTIONr_chiral_restr0.0910.21266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026162
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.23936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25587
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2312
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3771.55224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67428213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.02233446
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6714.52946
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.487→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 97 -
Rwork0.306 1968 -
obs--84.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8216-0.2626-0.061.3182-0.44892.0306-0.00510.10910.0137-0.06810.0344-0.0212-0.0026-0.0644-0.0293-0.10750.00640.0105-0.14640.0136-0.09331.9108-0.39683.7471
22.0640.3874-0.06571.63330.11441.9199-0.0233-0.1335-0.01450.0840.0311-0.0131-0.03350.1014-0.0078-0.0922-0.00670.0156-0.1366-0.0059-0.106425.2687-0.194728.5924
32.3776-0.79650.47572.6317-0.53072.7123-0.1484-0.0080.32820.1637-0.0541-0.0825-0.19380.060.2024-0.0875-0.0095-0.0228-0.07450.01-0.014132.483529.3095-1.2313
42.54270.66360.57922.87680.1912.4958-0.17370.0020.3577-0.148-0.04280.0922-0.1690.00930.2165-0.0756-0.0051-0.017-0.0694-0.0138-0.00578.937729.5898-26.4157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 260
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION2B5 - 260
4X-RAY DIFFRACTION2B301 - 302
5X-RAY DIFFRACTION3C5 - 261
6X-RAY DIFFRACTION3C301 - 302
7X-RAY DIFFRACTION4D5 - 260
8X-RAY DIFFRACTION4D301 - 302

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more