5CFU

Crystal Structure of ANT(2")-Ia in complex with adenylyl-2"-tobramycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of ANT(2")-Ia in complex with adenylyl-2"-tobramycin

Rodionov, D.Bassenden, A.V.Berghuis, A.M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside Nucleotidyltransferase (2")-Ia
A
185Pseudomonas aeruginosaMutation(s): 0 
Gene Names: aadB
Find proteins for Q6X3H6 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q6X3H6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

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Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
BU1
Query on BU1

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Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
51H
Query on 51H

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Download CCD File 
A
adenylyl-2"-tobramycin
(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxytetrahydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-phosphate (non-preferred name)
C28 H49 N10 O15 P
RHQLHNATZATWNZ-XMUWNKPOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.090α = 90.00
b = 41.910β = 105.08
c = 47.130γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling
StructureStudiodata collection
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaCIHR MOP-13107

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Derived calculations, Refinement description