5VMT

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of glyceraldehyde 3-phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis.

Barrett, K.F.Dranow, D.M.Phan, I.Q.Michaels, S.A.Shaheen, S.Navaluna, E.D.Craig, J.K.Tillery, L.M.Choi, R.Edwards, T.E.Conrady, D.G.Abendroth, J.Horanyi, P.S.Lorimer, D.D.Van Voorhis, W.C.Zhang, Z.Barrett, L.K.Subramanian, S.Staker, B.Fan, E.Myler, P.J.Soge, O.O.Hybiske, K.Ojo, K.K.

(2020) Protein Sci 29: 768-778

  • DOI: https://doi.org/10.1002/pro.3824
  • Primary Citation of Related Structures:  
    5VMT, 6OK4

  • PubMed Abstract: 

    Neisseria gonorrhoeae (Ng) and Chlamydia trachomatis (Ct) are the most commonly reported sexually transmitted bacteria worldwide and usually present as co-infections. Increasing resistance of Ng to currently recommended dual therapy of azithromycin and ceftriaxone presents therapeutic challenges for syndromic management of Ng-Ct co-infections. Development of a safe, effective, and inexpensive dual therapy for Ng-Ct co-infections is an effective strategy for the global control and prevention of these two most prevalent bacterial sexually transmitted infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a validated drug target with two approved drugs for indications other than antibacterials. Nonetheless, any new drugs targeting GAPDH in Ng and Ct must be specific inhibitors of bacterial GAPDH that do not inhibit human GAPDH, and structural information of Ng and Ct GAPDH will aid in finding such selective inhibitors. Here, we report the X-ray crystal structures of Ng and Ct GAPDH. Analysis of the structures demonstrates significant differences in amino acid residues in the active sites of human GAPDH from those of the two bacterial enzymes suggesting design of compounds to selectively inhibit Ng and Ct is possible. We also describe an efficient in vitro assay of recombinant GAPDH enzyme activity amenable to high-throughput drug screening to aid in identifying inhibitory compounds and begin to address selectivity.


  • Organizational Affiliation

    Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
342Neisseria gonorrhoeae NCCP11945Mutation(s): 0 
Gene Names: NGK_2321
EC: 1.2.1
UniProt
Find proteins for B4RPP8 (Neisseria gonorrhoeae (strain NCCP11945))
Explore B4RPP8 
Go to UniProtKB:  B4RPP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4RPP8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
L [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
V [auth H]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
K [auth A],
N [auth C],
P [auth D],
R [auth E],
T [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.45α = 90
b = 132.1β = 94.56
c = 156γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description