9NYA | pdb_00009nya

Solution NMR structure of SET-9/26 PHD finger in the peptide (H3K4me3)-bound state

PDB DOI: https://doi.org/10.2210/pdb9NYA/pdb
BMRB: 52907

Classification: GENE REGULATION
Organism(s): Caenorhabditis elegans, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-27 Released: 2026-10-14
Deposition Author(s): Monteiro, D., Jones, N., Ni, J., Becker, W., Lambrechts, L.S., Payne, R.J., Ashe, A.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 400
Conformers Submitted: 4
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 9NYA

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

Literature

Solution NMR structure of SET-9/26 PHD finger in the peptide (H3K4me3)-bound state

Monteiro, D., Jones, N., Ni, J., Becker, W., Lambrechts, L.S., Payne, R.J., Ashe, A.

To be published.

Macromolecule Content

Total Structure Weight: 12.77 kDa
Atom Count: 681
Modeled Residue Count: 86
Deposited Residue Count: 112
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD-type dom	A	92	Caenorhabditis elegans	Mutation(s): 0 Gene Names: set-9, F15E6.1 EC: 2.1.1
UniProt
Find proteins for O44498 (Caenorhabditis elegans) Explore O44498 Go to UniProtKB: O44498
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O44498
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K4me3 peptide	B	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NXT2 (Homo sapiens) Explore Q6NXT2 Go to UniProtKB: Q6NXT2
PHAROS: Q6NXT2 GTEx: ENSG00000188375
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NXT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
M3L Query on M3L	B	LYS	Methylation	C₉ H₂₁ N₂ O₂

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 400
Conformers Submitted: 4
Selection Criteria: structures with the lowest energy

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

Lambrechts, L.S.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP200102904

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release