[English] 日本語
Yorodumi
- PDB-9r2j: Crystal structure of human MAO B in complex with (E)-3-(4-nitroph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r2j
TitleCrystal structure of human MAO B in complex with (E)-3-(4-nitrophenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (chalcone inhibitor, 4a)
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / monoamine oxidase / chalcone / neuroprotective drug
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding / mitochondrial outer membrane / electron transfer activity / mitochondrion
Similarity search - Function
: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Chem-C15 / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMarchese, S. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Design, synthesis, and biological evaluation of chalcone derivatives as selective Monoamine Oxidase-B inhibitors with potential neuroprotective effects.
Authors: Facchetti, G. / Marchese, S. / Cocce, V. / Doneda, L. / Alessandri, G. / Paino, F. / Pessina, A. / Pinzi, L. / Rastelli, G. / Binda, C. / Christodoulou, M.S. / Rimoldi, I.
History
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Amine oxidase [flavin-containing] B
BBB: Amine oxidase [flavin-containing] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3008
Polymers117,4132
Non-polymers2,8876
Water15,367853
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-36 kcal/mol
Surface area36780 Å2
Unit cell
Length a, b, c (Å)132.342, 223.925, 86.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11AAA-1097-

HOH

21BBB-793-

HOH

31BBB-824-

HOH

41BBB-827-

HOH

51BBB-1000-

HOH

-
Components

#1: Protein Amine oxidase [flavin-containing] B / Monoamine oxidase type B / MAO-B


Mass: 58706.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The C-terminal portion (residues 502-520) of the protein is not visible in the electron density and therefore was not included in the structure file.
Source: (gene. exp.) Homo sapiens (human) / Gene: MAOB / Production host: Komagataella pastoris (fungus) / References: UniProt: P27338, monoamine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H38NO3S
#4: Chemical ChemComp-A1JCO / (~{E})-3-(4-nitrophenyl)-1-[3-(trifluoromethyl)phenyl]prop-2-en-1-one


Mass: 321.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10F3NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG4000, ADA buffer pH 6.5, 70 mM lithium sulphate, 8.5 mM Zwittergent 3-12

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→47.68 Å / Num. obs: 119203 / % possible obs: 100 % / Redundancy: 15.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.062 / Rrim(I) all: 0.174 / Net I/σ(I): 14.1
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 5849 / CC1/2: 0.823 / Rpim(I) all: 0.367 / Rrim(I) all: 1.032

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.842 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.087
RfactorNum. reflection% reflection
Rfree0.1727 3000 2.517 %
Rwork0.1442 116199 -
all0.145 --
obs-119199 99.952 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.854 Å2
Baniso -1Baniso -2Baniso -3
1-0.278 Å20 Å2-0 Å2
2---0.175 Å20 Å2
3----0.103 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 178 853 8957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177856
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.67911325
X-RAY DIFFRACTIONr_angle_other_deg1.8271.58818119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91621.655417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.138151415
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg20.79152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7021558
X-RAY DIFFRACTIONr_chiral_restr0.0920.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021854
X-RAY DIFFRACTIONr_nbd_refined0.2050.21462
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.27012
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23952
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2542
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.130.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined1.1160.21
X-RAY DIFFRACTIONr_nbd_other0.2850.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.227
X-RAY DIFFRACTIONr_mcbond_it1.6851.6773984
X-RAY DIFFRACTIONr_mcbond_other1.6791.6763983
X-RAY DIFFRACTIONr_mcangle_it2.3652.5044978
X-RAY DIFFRACTIONr_mcangle_other2.3682.5064979
X-RAY DIFFRACTIONr_scbond_it3.2672.0794340
X-RAY DIFFRACTIONr_scbond_other3.2672.0794341
X-RAY DIFFRACTIONr_scangle_it4.9712.9666344
X-RAY DIFFRACTIONr_scangle_other4.9712.9666345
X-RAY DIFFRACTIONr_lrange_it6.20920.5899342
X-RAY DIFFRACTIONr_lrange_other6.09820.0949154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.222160.1788522X-RAY DIFFRACTION99.9771
1.847-1.8970.2182220.1728261X-RAY DIFFRACTION99.9646
1.897-1.9520.2031950.1688119X-RAY DIFFRACTION99.988
1.952-2.0120.1772060.1557833X-RAY DIFFRACTION99.9627
2.012-2.0780.1751990.1487622X-RAY DIFFRACTION99.9617
2.078-2.1510.171680.1447367X-RAY DIFFRACTION99.9867
2.151-2.2320.1681800.1367162X-RAY DIFFRACTION99.9592
2.232-2.3240.1521640.1256881X-RAY DIFFRACTION99.9574
2.324-2.4270.1591700.1256553X-RAY DIFFRACTION100
2.427-2.5450.1661800.1316284X-RAY DIFFRACTION100
2.545-2.6830.1531670.1335990X-RAY DIFFRACTION100
2.683-2.8450.1591670.1335656X-RAY DIFFRACTION100
2.845-3.0420.1651330.145362X-RAY DIFFRACTION99.9636
3.042-3.2850.1651170.1344994X-RAY DIFFRACTION99.8632
3.285-3.5990.1681150.1434622X-RAY DIFFRACTION100
3.599-4.0230.1651100.1384180X-RAY DIFFRACTION100
4.023-4.6440.1681060.1333723X-RAY DIFFRACTION99.9739
4.644-5.6860.163840.1483147X-RAY DIFFRACTION99.9691
5.686-8.0310.171670.1772484X-RAY DIFFRACTION99.9217
8.031-47.680.29340.1961437X-RAY DIFFRACTION98.3947

+
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