8SHR | pdb_00008shr

Crystal Structure of PRMT3 with Compound YD1-214

PDB DOI: https://doi.org/10.2210/pdb8SHR/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-14 Released: 2024-04-17
Deposition Author(s): Song, X., Dong, A., Deng, Y., Huang, R., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.215 (Depositor), 0.233 (DCC)
R-Value Work:
0.185 (Depositor), 0.193 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of PRMT3 with Compound YD1-214

Song, X., Dong, A., Deng, Y., Huang, R., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 38.73 kDa
Atom Count: 2,574
Modeled Residue Count: 311
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 3	A	340	Homo sapiens	Mutation(s): 0 Gene Names: PRMT3, HRMT1L3 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for O60678 (Homo sapiens) Explore O60678 Go to UniProtKB: O60678
PHAROS: O60678 GTEx: ENSG00000185238
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60678
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIY (Subject of Investigation/LOI) Query on HIY 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]	5'-S-[2-(phenylcarbamamido)ethyl]-5'-thioadenosine C₁₉ H₂₃ N₇ O₄ S ZVEFVGBDFYZLDZ-SCFUHWHPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.215 (Depositor), 0.233 (DCC)
R-Value Work: 0.185 (Depositor), 0.193 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.211	α = 90
b = 70.211	β = 90
c = 175.142	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.