8SIG | pdb_00008sig

Crystal Structure of PRMT4 with Compound YD1-288

PDB DOI: https://doi.org/10.2210/pdb8SIG/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-04-16 Released: 2024-04-24
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: 1.78 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.183 (Depositor), 0.200 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of PRMT4 with Compound YD1-288

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: 41.47 kDa
Atom Count: 3,074
Modeled Residue Count: 333
Deposited Residue Count: 359
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-arginine methyltransferase CARM1	A	359	Homo sapiens	Mutation(s): 0 Gene Names: CARM1, PRMT4 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q86X55 (Homo sapiens) Explore Q86X55 Go to UniProtKB: Q86X55
PHAROS: Q86X55 GTEx: ENSG00000142453
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86X55
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GWU (Subject of Investigation/LOI) Query on GWU 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'-{(3-aminopropyl)[2-(benzylcarbamamido)ethyl]amino}-5'-deoxyadenosine C₂₃ H₃₃ N₉ O₄ XDYSZBVLXUKRDP-WGQQHEPDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [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] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]