5V9J

Crystal structure of catalytic domain of GLP with MS0105


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: experimental
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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

Crystal structure of catalytic domain of GLP with MS0105

Zeng, H.Dong, A.Liu, J.Xiong, Y.Babault, N.Jin, J.Tempel, W.Bountra, C.Arrowsmith, C.H.Edwards, A.M.Wu, H.Brown, P.J.Structural Genomics Consortium (SGC)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EHMT1
A, B
287Homo sapiensMutation(s): 0 
Gene Names: EHMT1EUHMTASE1GLPKIAA1876KMT1D
EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.367 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9B1 (Homo sapiens)
Explore Q9H9B1 
Go to UniProtKB:  Q9H9B1
PHAROS:  Q9H9B1
GTEx:  ENSG00000181090 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9B1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
90P
Query on 90P

Download Ideal Coordinates CCD File 
D [auth A],
S [auth B]
N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine
C24 H37 N5 O2
ROYAWJTXZUOQDE-UHFFFAOYSA-N
SAM
Query on SAM

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C [auth A],
R [auth B]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
DMS
Query on DMS

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Y [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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E [auth A]
F [auth A]
G [auth A]
H [auth A]
T [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

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I [auth A],
J [auth A],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
Z [auth B]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.848α = 90
b = 95.891β = 90
c = 102.416γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description