2HKM | pdb_00002hkm

Crystal structure of the Schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with phenylethylamine.

• PDB DOI: https://doi.org/10.2210/pdb2HKM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis
• Mutation(s): No 


• Deposited: 2006-07-05 Released: 2008-04-01 
• Deposition Author(s): Roujeinikova, A., Leys, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.161 (DCC) 

Literature

Structure-reactivity correlations and kinetic isotope effects in aromatic amine dehydrogenase

Hothi, P., Roujeinikova, A., Sutcliffe, M.J., Cullis, P., Leys, D., Scrutton, N.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 109.5 kDa 
• Atom Count: 8,692 
• Modeled Residue Count: 950 
• Deposited Residue Count: 994 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic amine dehydrogenase	A [auth D], B [auth H]	135	Alcaligenes faecalis	Mutation(s): 0  EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
UniProt
Find proteins for P84887 (Alcaligenes faecalis) Explore P84887  Go to UniProtKB:  P84887

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic amine dehydrogenase	C [auth A], D [auth B]	362	Alcaligenes faecalis	Mutation(s): 0  EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
UniProt
Find proteins for P84888 (Alcaligenes faecalis) Explore P84888  Go to UniProtKB:  P84888

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEA	E [auth D], F [auth H]	2-PHENYLETHYLAMINE C8 H12 N BHHGXPLMPWCGHP-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRQ	A [auth D], B [auth H]	L-PEPTIDE LINKING	C11 H10 N2 O4		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.161 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.398	α = 90
b = 89.109	β = 90.47
c = 80.082	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Roujeinikova, A., Leys, D.

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary