5RAB

PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001726a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library

Snee, M.Nowak, R.Johansson, C.Burgess-Brown, N.A.Arrowsmith, C.H.Bountra, C.Edwards, A.M.Oppermann, U.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 3B
A, B
372Homo sapiensMutation(s): 0 
Gene Names: KDM3BC5orf7JHDM2BJMJD1BKIAA1082
EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q7LBC6 (Homo sapiens)
Explore Q7LBC6 
Go to UniProtKB:  Q7LBC6
PHAROS:  Q7LBC6
GTEx:  ENSG00000120733 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7LBC6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S4Y (Subject of Investigation/LOI)
Query on S4Y

Download Ideal Coordinates CCD File 
C [auth A](2R,5S)-5-(4-chlorophenyl)oxolane-2-carbohydrazide
C11 H13 Cl N2 O2
ADMQSYHHBOTIMC-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.66α = 90
b = 93.64β = 107.8
c = 93.47γ = 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: 2020-04-22
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references