5NRI

Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP and D-Ala-D-Ala


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Characterisation of Burkholderia pseudomallei D-alanine-D-alanine ligase

Diaz-Saez, L.Hunter, W.N.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanine--D-alanine ligase
A, B
312Burkholderia pseudomallei (strain 1106a)Mutation(s): 0 
Gene Names: ddl
EC: 6.3.2.4
Find proteins for A3NZL3 (Burkholderia pseudomallei (strain 1106a))
Go to UniProtKB:  A3NZL3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DAL
Query on DAL

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A
D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
 Ligand Interaction
PGE
Query on PGE

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B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

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Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.642α = 90.00
b = 61.133β = 90.31
c = 69.972γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release