PDB-7zw3: Crystal Structure of human MAO B in complex with (Z)-N-benzyl-1-(...

ID or keywords:

Entry

Database: PDB / ID: 7zw3

Title

Crystal Structure of human MAO B in complex with (Z)-N-benzyl-1-(8-hydroxyquinolin-2-yl)methanimine oxide (inhibitor 19)

Components

Amine oxidase [flavin-containing] B

Keywords

FLAVOPROTEIN / Monoamine Oxidase / Alzheimer's disease / enzyme / drug / mitochondrial membrane

Function / homology

Function and homology information

Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Binda, C. / Gottinger, A.

Funding support

Italy, 1items

Citation

Journal: Acta Pharm Sin B / Year: 2023
Title: 8-Hydroxyquinolylnitrones as multifunctional ligands for the therapy of neurodegenerative diseases.
Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. ...

History

Deposition	May 18, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 29, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2023	Group: Database references / Category: citation Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7zw3.cif.gz	238.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7zw3.ent.gz		Display	PDB format
PDBx/mmJSON format	7zw3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zw/7zw3 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/7zw3	HTTPS FTP

-
Related structure data

Related structure data	7qbqC 7qbrC 7zpbC 2v5zS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#52 - Apr 2004 Growth Hormone similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (3)

Deposited unit

AAA: Amine oxidase [flavin-containing] B

BBB: Amine oxidase [flavin-containing] B

hetero molecules

120 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	131.644, 222.399, 86.221
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	21
Space group name H-M	C222

#1: Protein	Amine oxidase [flavin-containing] B / Monoamine oxidase type B / MAO-B Mass: 58837.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAOB / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71 / 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 / 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-AI0 / 1-(8-oxidanylquinolin-2-yl)-N-(phenylmethyl)methanimine oxide / (Z)-N-benzyl-1-(8-hydroxyquinolin-2-yl)methanimine oxide Mass: 278.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₁₄N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.13 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12 % (w/v) PEG 4000, 100 mM ADA buffer pH 6.5, 70 mM Lithium Sulfate, 4.5 mM Zwittergent 3-12

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 7, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.965459 Å / Relative weight: 1
Reflection	Resolution: 2→47.34 Å / Num. obs: 84901 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC_1/2: 0.99 / R_merge(I) obs: 0.17 / R_pim(I) all: 0.117 / R_rim(I) all: 0.207 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2→2.04 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.856 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4484 / CC_1/2: 0.617 / R_pim(I) all: 0.628 / R_rim(I) all: 0.99 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2V5Z

2v5z

Resolution: 2→47.34 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.933 / SU B: 3.725 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2042	2205	2.598 %
R_work	0.1661	82667	-
all	0.167	-	-
obs	-	84872	99.156 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 21.933 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.635 Å²	0 Å²	-0 Å²
2-	-	-1.223 Å²	0 Å²
3-	-	-	-0.412 Å²

Refinement step

Cycle: LAST / Resolution: 2→47.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7926	0	174	689	8789

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	8354
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	7902
X-RAY DIFFRACTION	r_angle_refined_deg	1.618	1.672	11370
X-RAY DIFFRACTION	r_angle_other_deg	1.764	1.584	18235
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.727	5	1011
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.018	21.655	417
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.969	15	1428
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	21.092	15	2
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.624	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	1061
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	9234
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1862
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	1677
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	7486
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	4033
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3627
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	567
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.178	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.373	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.278	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.628	0.2	33
X-RAY DIFFRACTION	r_mcbond_it	1.617	2.068	3996
X-RAY DIFFRACTION	r_mcbond_other	1.613	2.067	3995
X-RAY DIFFRACTION	r_mcangle_it	2.318	3.091	4996
X-RAY DIFFRACTION	r_mcangle_other	2.319	3.092	4997
X-RAY DIFFRACTION	r_scbond_it	2.688	2.435	4358
X-RAY DIFFRACTION	r_scbond_other	2.688	2.436	4359
X-RAY DIFFRACTION	r_scangle_it	4.158	3.53	6365
X-RAY DIFFRACTION	r_scangle_other	4.157	3.531	6366
X-RAY DIFFRACTION	r_lrange_it	5.52	24.91	9666
X-RAY DIFFRACTION	r_lrange_other	5.446	24.685	9536

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.052	0.262	185	0.236	6118	X-RAY DIFFRACTION	99.7468
2.052-2.108	0.252	137	0.223	5910	X-RAY DIFFRACTION	99.6047
2.108-2.169	0.218	151	0.204	5733	X-RAY DIFFRACTION	99.5938
2.169-2.236	0.22	154	0.185	5584	X-RAY DIFFRACTION	99.3249
2.236-2.309	0.213	144	0.177	5483	X-RAY DIFFRACTION	99.4697
2.309-2.39	0.171	136	0.161	5256	X-RAY DIFFRACTION	99.465
2.39-2.48	0.168	147	0.16	5019	X-RAY DIFFRACTION	99.3462
2.48-2.582	0.243	121	0.168	4906	X-RAY DIFFRACTION	99.3871
2.582-2.696	0.205	138	0.168	4676	X-RAY DIFFRACTION	99.3602
2.696-2.828	0.215	135	0.167	4457	X-RAY DIFFRACTION	99.3294
2.828-2.981	0.189	108	0.161	4311	X-RAY DIFFRACTION	99.7742
2.981-3.162	0.21	86	0.158	4084	X-RAY DIFFRACTION	99.8085
3.162-3.38	0.19	102	0.147	3772	X-RAY DIFFRACTION	98.2003
3.38-3.65	0.192	91	0.152	3515	X-RAY DIFFRACTION	98.3633
3.65-3.998	0.182	86	0.146	3265	X-RAY DIFFRACTION	98.7331
3.998-4.469	0.192	81	0.139	2980	X-RAY DIFFRACTION	98.7738
4.469-5.159	0.195	69	0.137	2650	X-RAY DIFFRACTION	98.8368
5.159-6.316	0.205	65	0.17	2218	X-RAY DIFFRACTION	98.2358
6.316-8.918	0.179	44	0.154	1744	X-RAY DIFFRACTION	97.2796
8.918-47.34	0.285	25	0.209	986	X-RAY DIFFRACTION	92.6673

-
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://pdbjlc1.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

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

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi