Macromolecule Content

Total Structure Weight: 50.57 kDa
Atom Count: 4016
Modelled Residue Count: 425
Deposited Residue Count: 429
Unique protein chains: 1

3QWP

Crystal structure of SET and MYND domain containing 3; Zinc finger MYND domain-containing protein 1

DOI: 10.2210/pdb3QWP/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-02-28 Released: 2011-04-06
Deposition Author(s): Dong, A., Dombrovski, L., Li, Y., Wernimont, A., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.217
R-Value Work: 0.174
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The Crystal Structure of human Histone-lysine N-methyltransferase SMYD3

Dombrovski, L., Dong, A., Wu, H., Min, J.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SET and MYND domain-containing protein 3	A	429	Homo sapiens	Mutation(s): 0 Gene Names: SMYD3, ZMYND1, ZNFN3A1 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
Find proteins for Q9H7B4 (Homo sapiens) Explore Q9H7B4 Go to UniProtKB: Q9H7B4
NIH Common Fund Data Resources
PHAROS: Q9H7B4 GTEx: ENSG00000185420
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain E [A] MOL2 format, chain E [A]	A	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain H [A] SDF format, chain I [A] SDF format, chain J [A] SDF format, chain K [A] SDF format, chain L [A] SDF format, chain M [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain J [A] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain M [A]	A	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [A] SDF format, chain C [A] SDF format, chain D [A] MOL2 format, chain B [A] MOL2 format, chain C [A] MOL2 format, chain D [A]	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.217
R-Value Work: 0.174
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.303	α = 90
b = 66.206	β = 90
c = 107.387	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2011-02-28
Released Date: 2011-04-06

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.