8X6L | pdb_00008x6l

PRMT5:MEP50 WITH SCR-6920 AND SAM

PDB DOI: https://doi.org/10.2210/pdb8X6L/pdb
EM Map EMD-38091: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-11-21 Released: 2025-02-26
Deposition Author(s): Zhou, F., Zhou, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

PRMT5:MEP50 WITH SCR-6920 AND SAM

Zhou, F., Zhou, F.

To be published.

Macromolecule Content

Total Structure Weight: 442.24 kDa
Atom Count: 29,724
Modeled Residue Count: 3,708
Deposited Residue Count: 3,916
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A, C, E, F	637	Homo sapiens	Mutation(s): 0 Gene Names: PRMT5 EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens) Explore O14744 Go to UniProtKB: O14744
PHAROS: O14744 GTEx: ENSG00000100462
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14744
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein WDR77	B, D, G, H	342	Homo sapiens	Mutation(s): 0 Gene Names: WDR77
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens) Explore Q9BQA1 Go to UniProtKB: Q9BQA1
PHAROS: Q9BQA1 GTEx: ENSG00000116455
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BQA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YFU (Subject of Investigation/LOI) Query on YFU Download Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain Q [auth E] SDF format, chain N [auth C] SDF format, chain K [auth A] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth C] MOL2 format, chain K [auth A] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth C] mmCIF format, chain K [auth A]	K [auth A], N [auth C], Q [auth E], T [auth F]	1-ethyl-8-[(2-methoxy-7-azaspiro[3.5]nonan-7-yl)carbonyl]-4-[2-oxidanylidene-2-[(3~{S})-1,2,3,4-tetrahydroisoquinolin-3-yl]ethyl]-2,3-dihydro-1,4-benzodiazepin-5-one C₃₂ H₄₀ N₄ O₄ QIAGGSLHFCTYMT-MHZLTWQESA-N		Interactions Focus chain K [auth A] Focus chain N [auth C] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain K [auth A] Focus chain N [auth C] Focus chain Q [auth E] Focus chain T [auth F]
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth F] SDF format, chain O [auth E] SDF format, chain L [auth C] MOL2 format, chain I [auth A] MOL2 format, chain R [auth F] MOL2 format, chain O [auth E] MOL2 format, chain L [auth C] mmCIF format, chain I [auth A] mmCIF format, chain R [auth F] mmCIF format, chain O [auth E] mmCIF format, chain L [auth C]	I [auth A], L [auth C], O [auth E], R [auth F]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain P [auth E] SDF format, chain M [auth C] SDF format, chain J [auth A] MOL2 format, chain S [auth F] MOL2 format, chain P [auth E] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] mmCIF format, chain S [auth F] mmCIF format, chain P [auth E] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A]	J [auth A], M [auth C], P [auth E], S [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth F]