6LGJ

Crystal structure of an oxido-reductase

• PDB DOI: https://doi.org/10.2210/pdb6LGJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-05 Released: 2020-12-09 
• Deposition Author(s): Yang, Y., Lei, J., Yin, L.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.216 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Crystal structure of an oxido-reductase

Yang, Y., Lei, J., Yin, L.

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 Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 146.06 kDa 
• Atom Count: 10,682 
• Modelled Residue Count: 1,332 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	333	Mus musculus	Mutation(s): 0  Gene Names: Gapdh, Gapd EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P16858 (Mus musculus) Explore P16858  Go to UniProtKB:  P16858
IMPC:  MGI:95640

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.216 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.14	α = 90
b = 112.17	β = 93.01
c = 84.83	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Yang, Y., Lei, J., Yin, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	--

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description