6ADE | pdb_00006ade

Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution

• PDB DOI: https://doi.org/10.2210/pdb6ADE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-07-31 Released: 2018-08-22 
• Deposition Author(s): Dilawari, R., Singh, P.K., Raje, M., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution

Dilawari, R., Singh, P.K., Raje, M., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 109.39 kDa 
• Atom Count: 7,679 
• Modeled Residue Count: 999 
• Deposited Residue Count: 1,005 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C	335	Homo sapiens	Mutation(s): 1  Gene Names: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P04406 (Homo sapiens) Explore P04406  Go to UniProtKB:  P04406
PHAROS:  P04406 GTEx:  ENSG00000111640

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B, C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.78	α = 90
b = 131.68	β = 90
c = 220.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Dilawari, R., Singh, P.K., Raje, M., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary