5QIT

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102821


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin thioesterase OTUB2A225Homo sapiensMutation(s): 0 
Gene Names: OTUB2C14orf137OTB2OTU2
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DC9 (Homo sapiens)
Explore Q96DC9 
Go to UniProtKB:  Q96DC9
PHAROS:  Q96DC9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J5J (Subject of Investigation/LOI)
Query on J5J

Download Ideal Coordinates CCD File 
B [auth A]N-[(E)-(3-methylphenyl)methylidene]acetamide
C10 H11 N O
KRUUSEWHYKJFLD-YRNVUSSQSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.289α = 90
b = 58.436β = 115.87
c = 49.713γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release