6VIP

TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008

• PDB DOI: https://doi.org/10.2210/pdb6VIP/pdb

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


• Deposited: 2020-01-13 Released: 2020-02-12 
• Deposition Author(s): The, J., Hong, Z., 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: 1.36 Å
• R-Value Free: 0.211 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008

The, J., Hong, Z., 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: 28.9 kDa 
• Atom Count: 2,135 
• Modelled Residue Count: 241 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TP53-binding protein 1	A, B	125	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
QXY (Subject of Investigation/LOI)	C [auth A], F [auth B]	{4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]phenyl}(4-ethylpiperazin-1-yl)methanone C19 H26 N4 O XFIDMUXINICVOV-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], G [auth B], H [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.211 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.887	α = 90
b = 60.156	β = 90
c = 69.721	γ = 90

Software Package:

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

Structure Validation

Currently 6VIP does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): The, J., Hong, Z., 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: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description