8RBK | pdb_00008rbk

Bos taurus PRMT9 in the presence of SAH

PDB DOI: https://doi.org/10.2210/pdb8RBK/pdb

Classification: TRANSFERASE
Organism(s): Bos taurus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-12-04 Released: 2024-12-11
Deposition Author(s): Bonnefond, L., Cavarelli, J.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.279 (Depositor), 0.275 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8RBK

Ligand Structure Quality Assessment

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

Literature

Crystal structure of PRMT9 with SAH

Bonnefond, L., Cavarelli, J.

To be published.

Macromolecule Content

Total Structure Weight: 93.49 kDa
Atom Count: 5,856
Modeled Residue Count: 738
Deposited Residue Count: 830
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MGC151858 protein	A	830	Bos taurus	Mutation(s): 0 Gene Names: PRMT9, MGC151858 EC: 2.1.1.320
UniProt
Find proteins for A5PJT3 (Bos taurus) Explore A5PJT3 Go to UniProtKB: A5PJT3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5PJT3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH 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-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.279 (Depositor), 0.275 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.433	α = 90
b = 121.247	β = 113.32
c = 67.355	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-19-CE11-0010-01

Revision History (Full details and data files)

Version 1.0: 2024-12-11
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.