7BJ1 | pdb_00007bj1

Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site

PDB DOI: https://doi.org/10.2210/pdb7BJ1/pdb
Entry: 7BJ1 supersedes: 6Z2R

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-01-13 Released: 2021-03-03
Deposition Author(s): Talibov, V.O., Cederfelt, D., Dobritzsch, D., Danielson, U.H.
Funding Organization(s): Swedish Research Council, Italian Association for Cancer Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.210 (Depositor), 0.214 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

Talibov, V.O., Fabini, E., FitzGerald, E.A., Tedesco, D., Cederfeldt, D., Talu, M.J., Rachman, M.M., Mihalic, F., Manoni, E., Naldi, M., Sanese, P., Forte, G., Barril, X., Simone, C., Bartolini, M., Dobritzsch, D., Danielson, U.H.

(2021) Chembiochem 22: 1597-1608

DOI: https://doi.org/10.1002/cbic.202000736

Macromolecule Content

Total Structure Weight: 50.75 kDa
Atom Count: 4,048
Modeled Residue Count: 426
Deposited Residue Count: 431
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SMYD3	A	431	Homo sapiens	Mutation(s): 2 Gene Names: SMYD3, ZMYND1, ZNFN3A1 EC: 2.1.1.354
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens) Explore Q9H7B4 Go to UniProtKB: Q9H7B4
PHAROS: Q9H7B4 GTEx: ENSG00000185420
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H7B4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
QKT (Subject of Investigation/LOI) Query on QKT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Diperodon (S-enantiomer) C₂₂ H₂₇ N₃ O₄ YUGZHQHSNYIFLG-FQEVSTJZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.210 (Depositor), 0.214 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.909	α = 90
b = 66.05	β = 90
c = 107.277	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

This entry supersedes: 6Z2R

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	D0571301
Italian Association for Cancer Research	Italy	19172

Revision History (Full details and data files)

Version 1.0: 2021-03-03
Type: Initial release
Version 1.1: 2021-03-10
Changes: Advisory
Version 1.2: 2021-03-17
Changes: Advisory
Version 1.3: 2021-10-06
Changes: Data collection, Database references, Structure summary
Version 1.4: 2024-01-31
Changes: Data collection, Refinement description

7BJ1 | pdb_00007bj1

Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site

Literature

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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