7U56

Crystal Structure of D-alanine--D-alanine ligase from Klebsiella pneumoniae subsp. pneumoniae in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal Structure of D-alanine--D-alanine ligase from Klebsiella pneumoniae subsp. pneumoniae in complex with AMP

Abendroth, J.Bolejack, M.J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-alanine--D-alanine ligaseA, B384Klebsiella pneumoniae subsp. pneumoniae HS11286Mutation(s): 0 
Gene Names: ddlKPHS_10610
EC: 6.3.2.4
UniProt
Find proteins for A0A0H3GSI5 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286))
Explore A0A0H3GSI5 
Go to UniProtKB:  A0A0H3GSI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3GSI5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
Q [auth B],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.35α = 90
b = 115.42β = 90
c = 68.48γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700059C

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release