2IIP

Human Nicotinamide N-methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb2IIP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-28 Released: 2006-10-10 
• Deposition Author(s): Bernstein, G., Min, J., Wu, H., Tempel, W., Zeng, H., Loppnau, P., Avvakumov, G.V., Wasney, G., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.265 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

The Crystal Structure of Human Nicotinamide N-methyltransferase in complex with SAH

Bernstein, G., Min, J., Wu, H., Tempel, W., Zeng, H., Loppnau, P., Avvakumov, G.V., Wasney, G., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 127.4 kDa 
• Atom Count: 8,481 
• Modelled Residue Count: 1,031 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide N-methyltransferase	A, B, C, D	283	Homo sapiens	Mutation(s): 3  Gene Names: NNMT EC: 2.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P40261 (Homo sapiens) Explore P40261  Go to UniProtKB:  P40261
PHAROS:  P40261 GTEx:  ENSG00000166741

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], F [auth B], G [auth C], H [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB:  2IIP	IC50: min: 2.63e+4, max: 3.53e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.265 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.016	α = 82.35
b = 62.007	β = 81.89
c = 107.073	γ = 68.3

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Bernstein, G., Min, J., Wu, H., Tempel, W., Zeng, H., Loppnau, P., Avvakumov, G.V., Wasney, G., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-21
  Changes: Data collection