5IZD | pdb_00005izd

Wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb5IZD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-25 Released: 2017-04-05 
• Deposition Author(s): Iermak, I., Mesters, J.R., Kuta Smatanova, I.
• Funding Organization(s): Czech Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure of wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP

Iermak, I., Mesters, J.R., Steffler, F., Sieber, V., Kuta Smatanova, I.

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: 456.85 kDa 
• Atom Count: 31,616 
• Modeled Residue Count: 3,925 
• Deposited Residue Count: 4,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glyceraldehyde dehydrogenase (NADP(+))	A, B, C, D, E, F, G, H	508	Thermoplasma acidophilum	Mutation(s): 0  Gene Names: Ta0809 EC: 1.2.1.89
UniProt
Find proteins for Q9HK01 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HK01  Go to UniProtKB:  Q9HK01

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	I [auth A], J [auth B], K [auth C], L [auth D], M [auth G], N [auth H]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.289	α = 90
b = 152.353	β = 92.19
c = 149.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
BALBES	phasing
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Iermak, I., Mesters, J.R., Kuta Smatanova, I.

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Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	DAAD-16-09

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Data collection
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary