4K9D

X-ray crystal structure of a Glyceraldehyde 3-phosphate dehydrogenase from Brugia malayi bound to the co-factor NAD

• PDB DOI: https://doi.org/10.2210/pdb4K9D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brugia malayi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-19 Released: 2013-05-01 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

X-ray crystal structure of a Glyceraldehyde 3-phosphate dehydrogenase from Brugia malayi bound to the co-factor NAD

Fairman, J.W., Fox, D., Lukacs, C.M., Edwards, T.E., Lorimer, D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 303.88 kDa 
• Atom Count: 20,811 
• Modelled Residue Count: 2,684 
• Deposited Residue Count: 2,776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D, E, F, G, H	347	Brugia malayi	Mutation(s): 0  Gene Names: Bm1_41940 EC: 1.2.1.12
UniProt
Find proteins for P48812 (Brugia malayi) Explore P48812  Go to UniProtKB:  P48812

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	I [auth A], L [auth B], N [auth C], P [auth D], Q [auth E], R [auth F], T [auth G], V [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO	J [auth A], K [auth A], M [auth B], O [auth C], S [auth F], U [auth G]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34K9D

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.76	α = 90
b = 176.99	β = 101.12
c = 94.25	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description