Macromolecule Content

Total Structure Weight: 61.73 kDa
Atom Count: 4771
Modelled Residue Count: 512
Deposited Residue Count: 548
Unique protein chains: 2

1XQH

Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH

DOI: 10.2210/pdb1XQH/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2004-10-12 Released: 2004-11-23
Deposition Author(s): Chuikov, S., Kurash, J.K., Wilson, J.R., Xiao, B., Justin, N., Ivanov, G.S., McKinney, K., Tempst, P., Prives, C., Gamblin, S.J., Barlev, N.A., Reinberg, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.223
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Regulation of p53 activity through lysine methylation

Chuikov, S., Kurash, J.K., Wilson, J.R., Xiao, B., Justin, N., Ivanov, G.S., McKinney, K., Tempst, P., Prives, C., Gamblin, S.J., Barlev, N.A., Reinberg, D.

(2004) Nature 432: 353-360

PubMed: 15525938 Search on PubMed
DOI: 10.1038/nature03117
Primary Citation of Related Structures:
1XQH

PubMed Abstract:

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-4 specific	A, C [auth E]	264	Homo sapiens	Mutation(s): 0 Gene Names: SETD7, KIAA1717, KMT7, SET7, SET9 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTS6 (Homo sapiens) Explore Q8WTS6 Go to UniProtKB: Q8WTS6
PHAROS: Q8WTS6 GTEx: ENSG00000145391
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
9-mer peptide from tumor protein p53	B, D [auth F]	10	N/A	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637
PHAROS: P04637 GTEx: ENSG00000141510
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth E] MOL2 format, chain E [auth A] MOL2 format, chain F [auth E]	E [auth A], F [auth E]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ Query on MLZ	B, D [auth F]	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SAH	IC50: 30000 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.223
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.374	α = 90
b = 103.123	β = 90.04
c = 67.165	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2004-10-12
Released Date: 2004-11-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-11-23
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 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.