3ZDF | pdb_00003zdf

Structure of GAPDH with CP12 peptide from Thermosynechococcus elongatus

• PDB DOI: https://doi.org/10.2210/pdb3ZDF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermosynechococcus vestitus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-26 Released: 2013-12-11 
• Deposition Author(s): Cotton, C.A.R., Murray, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure of Gapdh

Cotton, C.A.R., Murray, J.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 83.96 kDa 
• Atom Count: 5,759 
• Modeled Residue Count: 720 
• Deposited Residue Count: 754 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE	A, B	354	Thermosynechococcus vestitus	Mutation(s): 0  EC: 1.2.1.13 (PDB Primary Data), 1.2.1 (UniProt)
UniProt
Find proteins for Q8DIW5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIW5  Go to UniProtKB:  Q8DIW5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CP12 POLYPEPTIDE	C, D	23	Thermosynechococcus vestitus	Mutation(s): 0
UniProt
Find proteins for Q8DHX3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DHX3  Go to UniProtKB:  Q8DHX3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.45	α = 90
b = 141.45	β = 90
c = 77.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Cotton, C.A.R., Murray, J.W.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary