4J7F

SET7/9Y335pAF in complex with TAF10 peptide and AdoHcy

PDB DOI: https://doi.org/10.2210/pdb4J7F/pdb

Classification: TRANSFERASE/PEPTIDE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-02-13 Released: 2014-03-26
Deposition Author(s): Horowitz, S., Del Rizzo, P.A., Trievel, R.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.215
R-Value Work: 0.201
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Methyl CH O Hydrogen Bonds Orchestrate AdoMet-Dependent Methylation

Horowitz, S., Dirk, L.M.A., Yesselman, J.D., Nimtz, J.S., Del Rizzo, P.A., Vander Meulen, K.A., Butcher, S.E., Mehl, R.A., Houtz, R.L., Al-Hashimi, H.M., Trievel, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 30.68 kDa
Atom Count: 2,137
Modelled Residue Count: 247
Deposited Residue Count: 272
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETD7	A	261	Homo sapiens	Mutation(s): 1 Gene Names: SETD7, KIAA1717, KMT7, SET7, SET9 EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTS6 (Homo sapiens) Explore Q8WTS6 Go to UniProtKB: Q8WTS6
PHAROS: Q8WTS6 GTEx: ENSG00000145391
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WTS6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 10	B	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q12962 (Homo sapiens) Explore Q12962 Go to UniProtKB: Q12962
PHAROS: Q12962 GTEx: ENSG00000166337
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12962
Sequence Annotations 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 C [auth A] MOL2 format, chain C [auth A]	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HOX Query on HOX	A	L-PEPTIDE LINKING	C₉ H₁₂ N₂ O₂		PHE

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB: 4J7F	IC50: min: 3.00e+4, max: 4.70e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.215
R-Value Work: 0.201
R-Value Observed: 0.202
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.046	α = 90
b = 83.046	β = 90
c = 95.524	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Del Rizzo, P.A.

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release

RCSB PDB Core Operations are 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.