8CNC

Structure of compound 1 bound KMT9

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-02-22 Released: 2024-03-06 
  • Deposition Author(s): Sheng, W.
  • Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Structure of compound 1 bound KMT9

Sheng, W., Eric, M., Roland, S.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
Find similar proteins by: 
(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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6D6
Query on 6D6
Download Ideal Coordinates CCD File 
C [auth A]5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine
C17 H28 N8 O5
NHAKJKNYYCYZBR-UOYPZJKHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.344α = 90
b = 110.344β = 90
c = 129.875γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-03-06 
    • Deposition Author(s): Sheng, W.
Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB850
German Research Foundation (DFG)GermanySFB992
German Research Foundation (DFG)GermanySFB1381
German Research Foundation (DFG)GermanySchu688/15-1
German Research Foundation (DFG)GermanyFR01-374
German Research Foundation (DFG)GermanyEXC-2189

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release