6AZE

Crystal Structure of the BPTF PHD-bromodomain module bound to H3KC4me3 methyl lysine analog

  • Classification: GENE REGULATION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-09-11 Released: 2018-09-19 
  • Deposition Author(s): Chen, Z., Ruthenburg, A.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), American Cancer Society

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Quantitative and structural assessment of methyllysine analog engagement by cognate binding proteins reveals decrements that can impact qualitative experiment interpretation

Chen, Z.Ruthenburg, A.J.Notti, R.Q.Ueberheide, B.Banaszynski, L.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleosome-remodeling factor subunit BPTFA167Homo sapiensMutation(s): 0 
Gene Names: BPTFFAC1FALZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens)
Explore Q12830 
Go to UniProtKB:  Q12830
PHAROS:  Q12830
GTEx:  ENSG00000171634 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12830
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ARG-THR-ML3-GLN-THRB [auth P]6Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
UniProt GroupP68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ML3
Query on ML3
B [auth P]L-PEPTIDE LINKINGC8 H19 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.263α = 90
b = 64.13β = 90
c = 85.67γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM115945
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR21HG007426
American Cancer SocietyUnited States130230- RSG-16-248-01-DMC

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence