6PVA

The structure of NTMT1 in complex with compound 11

• PDB DOI: https://doi.org/10.2210/pdb6PVA/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-20 Released: 2020-08-19 
• Deposition Author(s): Noinaj, N., Chen, D., Huang, R.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.232 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

The structure of NTMT1 in complex with compound 11

Chen, D., Noinaj, N., Huang, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 28.14 kDa 
• Atom Count: 2,001 
• Modelled Residue Count: 231 
• Deposited Residue Count: 247 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal Xaa-Pro-Lys N-methyltransferase 1	A [auth B]	241	Homo sapiens	Mutation(s): 0  Gene Names: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 EC: 2.1.1.244
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BV86 (Homo sapiens) Explore Q9BV86  Go to UniProtKB:  Q9BV86
PHAROS:  Q9BV86 GTEx:  ENSG00000148335

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINO GROUP-()-LYSINE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine	B [auth A]	6	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GLZ	B [auth A]	L-PEPTIDE LINKING	C2 H5 N O		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.232 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.012	α = 90
b = 73.012	β = 90
c = 82.172	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Noinaj, N., Chen, D., Huang, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1U01CA214649-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM117275-01A1

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2021-04-21
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection