6G5N

Crystal structure of human SP100 in complex with bromodomain-focused fragment XS039818e 1-(3-Phenyl-1,2,4-oxadiazol-5-yl)methanamine

• PDB DOI: https://doi.org/10.2210/pdb6G5N/pdb

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


• Deposited: 2018-03-29 Released: 2018-04-11 
• Deposition Author(s): Talon, R.P.H., Krojer, T., Tallant, C., Nunez-Alonso, G., Fairhead, M., Szykowska, A., Collins, P., Pearce, N.M., Ng, J., MacLean, E., Wright, N., Douangamath, A., Brandao-Neto, J., Burgess-Brown, N., Huber, K., Knapp, S., Brennan, P.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: other

Literature

Identifying small molecule binding sites for epigenetic proteins at domain-domain interfaces

Talon, R.P.H., Bowkett, D., Tallant, C., Schofield, C., von Delft, F., Knapp, S., Bruton, G., Brennan, P.E.

(2018) bioRxiv 

• DOI: https://doi.org/10.1101/283069

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.91 kDa 
• Atom Count: 3,422 
• Modelled Residue Count: 347 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear autoantigen Sp-100	A, B	180	Homo sapiens	Mutation(s): 0  Gene Names: SP100
UniProt & NIH Common Fund Data Resources
Find proteins for P23497 (Homo sapiens) Explore P23497  Go to UniProtKB:  P23497
PHAROS:  P23497 GTEx:  ENSG00000067066

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ENK (Subject of Investigation/LOI)	H [auth A]	(3-phenyl-1,2,4-oxadiazol-5-yl)methanamine C9 H9 N3 O QFBMJBDECSEYCZ-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.879	α = 90
b = 45.426	β = 102.14
c = 83.477	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Talon, R.P.H., Krojer, T., Tallant, C., Nunez-Alonso, G., Fairhead, M., Szykowska, A., Collins, P., Pearce, N.M., Ng, J., MacLean, E., Wright, N., Douangamath, A., Brandao-Neto, J., Burgess-Brown, N., Huber, K., Knapp, S., Brennan, P.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F.

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Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary