2BT3 | pdb_00002bt3

AGAO in complex with Ruthenium-C4-wire at 1.73 angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.171 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.154 (Depositor) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Reversible Inhibition of Copper Amine Oxidase Activity by Channel-Blocking Ruthenium(II) and Rhenium(I) Molecular Wires.

Contakes, S.M.Juda, G.A.Langley, D.B.Halpern-Manners, N.W.Duff, A.P.Dunn, A.R.Gray, H.B.Dooley, D.M.Guss, J.M.Freeman, H.C.

(2005) Proc Natl Acad Sci U S A 102: 13451

  • DOI: https://doi.org/10.1073/pnas.0506336102
  • Primary Citation Related Structures: 
    2BT3

  • PubMed Abstract: 

    Molecular wires comprising a Ru(II)- or Re(I)-complex head group, an aromatic tail group, and an alkane linker reversibly inhibit the activity of the copper amine oxidase from Arthrobacter globiformis (AGAO), with K(i) values between 6 muM and 37 nM. In the crystal structure of a Ru(II)-wire:AGAO conjugate, the wire occupies the AGAO active-site substrate access channel, the trihydroxyphenylalanine quinone cofactor is ordered in the "off-Cu" position with its reactive carbonyl oriented toward the inhibitor, and the "gate" residue, Tyr-296, is in the "open" position. Head groups, tail-group substituents, and linker lengths all influence wire-binding interactions with the enzyme.


  • Organizational Affiliation
    • Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 73.5 kDa 
  • Atom Count: 5,553 
  • Modeled Residue Count: 620 
  • Deposited Residue Count: 646 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHENYLETHYLAMINE OXIDASE646Arthrobacter globiformisMutation(s): 0 
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for P46881 (Arthrobacter globiformis)
Explore P46881 
Go to UniProtKB:  P46881
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46881
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R4A

Query on R4A



Download:Ideal Coordinates CCD File
D [auth A]BIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~]{3-[4-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)BUTOXY]-N,N-DIMETHYLANILINATO(2-)}RUTHENIUM
C44 H61 N7 O Ru
LKBNPCYTIAPTEX-RKQPFBAPSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
B [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPQ
Query on TPQ
A
L-PEPTIDE LINKINGC9 H9 N O5TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.171 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.154 (Depositor) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.059α = 90
b = 62.905β = 112.11
c = 92.097γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description