4MIK | pdb_00004mik

Crystal Structure of hPNMT in Complex with bisubstrate inhibitor (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-(((2-(((7-nitro-1,2,3,4-tetrahydroisoquinolin-3-yl)methyl)amino)ethyl)thio)methyl)tetrahydrofuran-3,4-diol

• PDB DOI: https://doi.org/10.2210/pdb4MIK/pdb

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


• Deposited: 2013-08-31 Released: 2014-09-10 
• Deposition Author(s): Bart, A.G., Scott, E.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 

Literature

To be published

Bart, A.G., Scott, E.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 64.97 kDa 
• Atom Count: 4,492 
• Modeled Residue Count: 520 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethanolamine N-methyltransferase	A, B	289	Homo sapiens	Mutation(s): 0  Gene Names: PNMT, PENT EC: 2.1.1.28
UniProt & NIH Common Fund Data Resources
Find proteins for P11086 (Homo sapiens) Explore P11086  Go to UniProtKB:  P11086
PHAROS:  P11086 GTEx:  ENSG00000141744

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JIL	C [auth A], E [auth B]	9-{5-S-[2-({[(3S)-7-nitro-1,2,3,4-tetrahydroisoquinolin-3-yl]methyl}amino)ethyl]-5-thio-alpha-L-lyxofuranosyl}-9H-purin-6-amine C22 H28 N8 O5 S XTRSLZMJUJDRCM-RWAFIUBPSA-N
TRS	D [auth A], F [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.664	α = 90
b = 94.664	β = 90
c = 188.46	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Bart, A.G., Scott, E.E.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Derived calculations
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary