2YSM | pdb_00002ysm

Solution structure of the second and third PHD domain from Histone-lysine N-methyltransferase 2C (KMT2C/MLL3)

PDB DOI: https://doi.org/10.2210/pdb2YSM/pdb
BMRB: 11237

Classification: TRANSFERASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2007-04-03 Released: 2007-10-09
Deposition Author(s): Qin, X.R., Hayashi, F., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function

wwPDB Validation 3D Report Full Report

Validation slider image for 2YSM

This is version 1.3 of the entry. See complete history.

Literature

Solution structure of the first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog

Qin, X.R., Hayashi, F., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 12.14 kDa
Atom Count: 819
Modeled Residue Count: 111
Deposited Residue Count: 111
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog	A	111	Homo sapiens	Mutation(s): 0 Gene Names: MLL3, HALR, KIAA1506 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEZ4 (Homo sapiens) Explore Q8NEZ4 Go to UniProtKB: Q8NEZ4
PHAROS: Q8NEZ4 GTEx: ENSG00000055609
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NEZ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-09

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-10-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-03-21
Changes: Derived calculations, Source and taxonomy, Structure summary
Version 1.3: 2024-05-01
Changes: Data collection, Database references, Derived calculations

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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.