7YF2

Crystal structure of METTL9 in complex with unmethylated SLC39A5 peptide and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for METTL9-mediated N1-histidine methylation.

Wang, X.Xie, H.Guo, Q.Cao, D.Ru, W.Zhao, S.Zhu, Z.Zhang, J.Pan, W.Yao, X.Xu, C.

(2023) Cell Discov 9: 38-38


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-L-histidine N-pros-methyltransferase
A, B
275Homo sapiensMutation(s): 6 
Gene Names: METTL9DREVCGI-81
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1A3 (Homo sapiens)
Explore Q9H1A3 
Go to UniProtKB:  Q9H1A3
PHAROS:  Q9H1A3
GTEx:  ENSG00000197006 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1A3
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SLC39A5 peptide
C, D
13Homo sapiensMutation(s): 0 
Gene Names: METTL9DREVCGI-81
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMH5 (Homo sapiens)
Explore Q6ZMH5 
Go to UniProtKB:  Q6ZMH5
PHAROS:  Q6ZMH5
GTEx:  ENSG00000139540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZMH5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.838α = 90
b = 45.836β = 122.64
c = 106.415γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-08
    Changes: Database references