6UPT | pdb_00006upt

Tudor Domain of Tumor suppressor p53BP1 with MFP-2706

• PDB DOI: https://doi.org/10.2210/pdb6UPT/pdb

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


• Deposited: 2019-10-18 Released: 2019-11-20 
• Deposition Author(s): The, J., Dong, A., Headey, S., Gunzburg, M., Doak, B., James, L.I., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Tudor Domain of Tumor suppressor p53BP1 with MFP-2706

The, J., Dong, A., Headey, S., Gunzburg, M., Doak, B., James, L.I., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.36 kDa 
• Atom Count: 1,937 
• Modeled Residue Count: 239 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TP53-binding protein 1	A, B	124	Homo sapiens	Mutation(s): 0  Gene Names: TP53BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12888 (Homo sapiens) Explore Q12888  Go to UniProtKB:  Q12888
PHAROS:  Q12888 GTEx:  ENSG00000067369

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QFM (Subject of Investigation/LOI)	C [auth A]	2-((2-chlorobenzyl)thio)-4,5-dihydro-1H-imidazole C10 H11 Cl N2 S MRKZZXDCOQKXGF-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.05	α = 90
b = 125.05	β = 90
c = 125.05	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): The, J., Dong, A., Headey, S., Gunzburg, M., Doak, B., James, L.I., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description