2E6R | pdb_00002e6r

Solution structure of the PHD domain in SmcY protein

PDB DOI: https://doi.org/10.2210/pdb2E6R/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2006-12-28 Released: 2007-07-03
Deposition Author(s): Kadirvel, S., He, F., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., 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 2E6R

This is version 1.4 of the entry. See complete history.

Literature

Solution structure of the PHD domain in SmcY protein

Kadirvel, S., He, F., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 10.15 kDa
Atom Count: 700
Modeled Residue Count: 92
Deposited Residue Count: 92
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Jumonji/ARID domain-containing protein 1D	A	92	Homo sapiens	Mutation(s): 0 Gene Names: JARID1D, HY, HYA, KIAA0234, SMCY EC: 1.14.11.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY66 (Homo sapiens) Explore Q9BY66 Go to UniProtKB: Q9BY66
PHAROS: Q9BY66 GTEx: ENSG00000012817
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BY66
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 B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [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: 2007-07-03

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-07-03
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2022-03-09
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-05-29
Changes: Data collection

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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.