6DUX | pdb_00006dux

2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.191 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L.Kochan, T.J.Minasov, G.Wawrzak, Z.Chang, C.Tan, K.Shuvalova, L.Kiryukhina, O.Pshenychnyi, S.Wu, R.Dubrovska, I.Babnigg, G.Endres, M.Anderson, W.F.Hauser, A.R.Joachimiak, A.Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322

  • DOI: https://doi.org/10.1128/mra.01013-22
  • Primary Citation of Related Structures:  
    6DT3, 6DUX, 6DVV, 6DXN, 6E85, 6NAU, 6NBG, 6NDI, 6WN5, 6WN8, 6X1L, 7RJJ, 7TL5, 7TZP

  • PubMed Abstract: 

    Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.


  • Organizational Affiliation
    • Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phospho-alpha-glucosidase
A, B
443Klebsiella pneumoniaeMutation(s): 0 
Gene Names: aglB
EC: 3.2.1.122
UniProt
Find proteins for Q9AGA6 (Klebsiella pneumoniae)
Explore Q9AGA6 
Go to UniProtKB:  Q9AGA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AGA6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
LMR
Query on LMR

Download Ideal Coordinates CCD File 
D [auth A](2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
I [auth B]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.226α = 90
b = 85.226β = 90
c = 228.858γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary