5DDI | pdb_00005ddi

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo enzyme - at 2.40 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5DDI/pdb

• Classification: OXIDOREDUCTASE, TRANSFERASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2015-08-24 Released: 2016-08-24 
• Deposition Author(s): Dimova, M., Devedjiev, Y.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.295 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Literature

Novel enhancer binding site found in bacteria and eukaryota but not in archea.

Dimova, M., Devedjiev, Y.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 109.82 kDa 
• Atom Count: 8,078 
• Modeled Residue Count: 996 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A [auth P], B [auth R], C [auth S]	332	Sus scrofa	Mutation(s): 0  EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt
Find proteins for P00355 (Sus scrofa) Explore P00355  Go to UniProtKB:  P00355

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth P], I [auth R], L [auth S]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	D [auth P], E [auth P], G [auth R], H [auth R], J [auth S], K [auth S]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.295 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.9	α = 90
b = 138.97	β = 90
c = 222.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Dimova, M., Devedjiev, Y.D.

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description