4J7F | pdb_00004j7f

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 (Depositor), 0.214 (DCC)
R-Value Work:
0.201 (Depositor), 0.199 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4J7F

Ligand Structure Quality Assessment

This is version 1.1 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
Modeled Residue Count: 247
Deposited Residue Count: 272
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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 (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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.215 (Depositor), 0.214 (DCC)
R-Value Work: 0.201 (Depositor), 0.199 (DCC)
R-Value Observed: 0.202 (Depositor)

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

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Ligand Structure Quality Assessment

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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
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.