6G5N | pdb_00006g5n

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.220 (Depositor), 0.222 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ENK (Subject of Investigation/LOI) Query on ENK Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(3-phenyl-1,2,4-oxadiazol-5-yl)methanamine C₉ H₉ N₃ O QFBMJBDECSEYCZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.220 (Depositor), 0.222 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History (Full details and data files)

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