6NM4

Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor

Ivanochko, D.Halabelian, L.Fischer, C.Sanders, J.M.Kattar, S.D.Brown, P.J.Edwards, A.M.Bountra, C.Arrowsmith, C.H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase PRDM9
A, B
191Homo sapiensMutation(s): 0 
Gene Names: PRDM9 (PFM6)
EC: 2.1.1.43
Find proteins for Q9NQV7 (Homo sapiens)
Go to Gene View: PRDM9
Go to UniProtKB:  Q9NQV7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
KS7
Query on KS7

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A, B
4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane
C25 H32 N6 O3
NZYTZRHHBAJPKN-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

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A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 38.026α = 90.00
b = 74.800β = 90.00
c = 141.435γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release