8H43 | pdb_00008h43

Crystal structure of PHF1 Tudor domain in complex with hit 1

• PDB DOI: https://doi.org/10.2210/pdb8H43/pdb

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


• Deposited: 2022-10-10 Released: 2023-10-18 
• Deposition Author(s): Liu, Y., Ruan, K.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.289 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Literature

Crystal structure of PHF1 Tudor domain in complex with hit 1

Liu, Y., Ruan, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.65 kDa 
• Atom Count: 1,393 
• Modeled Residue Count: 171 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger protein 1	A, B, C	61	Homo sapiens	Mutation(s): 0  Gene Names: PHF1
UniProt & NIH Common Fund Data Resources
Find proteins for O43189 (Homo sapiens) Explore O43189  Go to UniProtKB:  O43189
PHAROS:  O43189 GTEx:  ENSG00000112511

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1HI (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	2-[(3S)-piperidin-3-yl]-1,3-benzoxazole C12 H14 N2 O MNJITFGKRQIUJN-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.289 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.718	α = 90
b = 42.718	β = 90
c = 401.905	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Liu, Y., Ruan, K.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21874123
National Natural Science Foundation of China (NSFC)	China	32090040

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release