9FKE | pdb_00009fke

SAH bound KMT9 crystal structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.203 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Literature

compound 1a bound KMT9 crystal structure

Sheng, W., Eric, M., Roland, S.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltransferase N6AMT1203Homo sapiensMutation(s): 0 
Gene Names: N6AMT1, C21orf127, HEMK2, KMT9, PRED28
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5N5 (Homo sapiens)
Explore Q9Y5N5 
Go to UniProtKB:  Q9Y5N5
PHAROS:  Q9Y5N5
GTEx:  ENSG00000156239 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5N5
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional methyltransferase subunit TRM112-like protein126Homo sapiensMutation(s): 0 
Gene Names: TRMT112, AD-001, HSPC152, HSPC170
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI30 (Homo sapiens)
Explore Q9UI30 
Go to UniProtKB:  Q9UI30
PHAROS:  Q9UI30
GTEx:  ENSG00000173113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI30
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH
Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.203 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.05α = 90
b = 110.05β = 90
c = 132.17γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB992
German Research Foundation (DFG)GermanySchu688
German Research Foundation (DFG)GermanyEXC-2189
German Research Foundation (DFG)GermanyDKTK FR01-374

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release