7TZP | pdb_00007tzp

Crystal Structure of Putataive Short-Chain Dehydrogenase/Reductase (FabG) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 in Complex with NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.191 (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
3-oxoacyl-ACP reductase
A, B, C, D, E
A, B, C, D, E, F, G, H
247Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044Mutation(s): 0 
Gene Names: fabG_6DBX64_14690SAMEA4364603_02057
EC: 1.1.1.100
UniProt
Find proteins for A0A332H2K8 (Klebsiella pneumoniae)
Explore A0A332H2K8 
Go to UniProtKB:  A0A332H2K8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A332H2K8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
AA [auth C],
MA [auth E],
O [auth A],
WA [auth G]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth G]
BA [auth C]
EB [auth H]
FA [auth D]
NA [auth E]
AB [auth G],
BA [auth C],
EB [auth H],
FA [auth D],
NA [auth E],
P [auth A],
Q [auth A],
R [auth A],
RA [auth F],
SA [auth F],
V [auth B],
W [auth B],
XA [auth G],
YA [auth G],
ZA [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BB [auth G]
CA [auth C]
CB [auth G]
FB [auth H]
GA [auth D]
BB [auth G],
CA [auth C],
CB [auth G],
FB [auth H],
GA [auth D],
GB [auth H],
HA [auth D],
HB [auth H],
OA [auth E],
PA [auth E],
QA [auth E],
S [auth A],
T [auth A],
X [auth B],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
I [auth A],
IA [auth E],
TA [auth G],
U [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth D]
DB [auth H]
EA [auth D]
J [auth A]
JA [auth E]
DA [auth D],
DB [auth H],
EA [auth D],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
N [auth A],
UA [auth G],
VA [auth G],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.387α = 90
b = 256.02β = 90
c = 260.642γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary