7W1E

Crystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide lyase in complex with products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.116 

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Ligand Structure Quality Assessment 


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Literature

Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use.

Tu, I.F.Lin, T.L.Yang, F.L.Lee, I.M.Tu, W.L.Liao, J.H.Ko, T.P.Wu, W.J.Jan, J.T.Ho, M.R.Chou, C.Y.Wang, A.H.Wu, C.Y.Wang, J.T.Huang, K.F.Wu, S.H.

(2022) J Biomed Sci 29: 9-9

  • DOI: https://doi.org/10.1186/s12929-022-00792-4
  • Primary Citation of Related Structures:  
    7W1C, 7W1D, 7W1E

  • PubMed Abstract: 

    K1 capsular polysaccharide (CPS)-associated Klebsiella pneumoniae is the primary cause of pyogenic liver abscesses (PLA) in Asia. Patients with PLA often have serious complications, ultimately leading to a mortality of ~ 5%. This K1 CPS has been reported as a promising target for development of glycoconjugate vaccines against K. pneumoniae infection. The pyruvylation and O-acetylation modifications on the K1 CPS are essential to the immune response induced by the CPS. To date, however, obtaining the fragments of K1 CPS that contain the pyruvylation and O-acetylation for generating glycoconjugate vaccines still remains a challenge.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
K1 LYASE
A, B, C, D, E
A, B, C, D, E, F
671Klebsiella phage NTUH-K2044-K1-1Mutation(s): 2 
UniProt
Find proteins for A0A068Q5Q5 (Klebsiella phage NTUH-K2044-K1-1)
Explore A0A068Q5Q5 
Go to UniProtKB:  A0A068Q5Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068Q5Q5
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
98X (Subject of Investigation/LOI)
Query on 98X

Download Ideal Coordinates CCD File 
BA [auth B]
FA [auth C]
JA [auth D]
KA [auth D]
PA [auth E]
BA [auth B],
FA [auth C],
JA [auth D],
KA [auth D],
PA [auth E],
QA [auth E],
V [auth A],
VA [auth F],
W [auth A],
X [auth A]
2,6-anhydro-4,5-O-[(1R)-1-carboxyethylidene]-3-deoxy-L-threo-hex-2-enonic acid
C9 H10 O7
ILHRGDJLAZPQBR-QKVARQBESA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth C]
DA [auth C]
HA [auth D]
IA [auth D]
AA [auth B],
CA [auth C],
DA [auth C],
HA [auth D],
IA [auth D],
LA [auth E],
OA [auth E],
R [auth A],
RA [auth F],
S [auth A],
SA [auth F],
U [auth A],
UA [auth F],
Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD (Subject of Investigation/LOI)
Query on IMD

Download Ideal Coordinates CCD File 
EA [auth C]
GA [auth D]
MA [auth E]
NA [auth E]
Q [auth A]
EA [auth C],
GA [auth D],
MA [auth E],
NA [auth E],
Q [auth A],
T [auth A],
TA [auth F],
Z [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.116 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.626α = 80.4
b = 100.991β = 70.48
c = 125.38γ = 83.99
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST-108-2113-M-001-008
Academia Sinica (Taiwan)TaiwanAS-KPQ-110-ITAR-11

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release