2PLA | pdb_00002pla

Crystal structure of human glycerol-3-phosphate dehydrogenase 1-like protein

• PDB DOI: https://doi.org/10.2210/pdb2PLA/pdb

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


• Deposited: 2007-04-19 Released: 2007-05-01 
• Deposition Author(s): Uppenberg, J., Smee, C., Hozjan, V., Kavanagh, K., Bunkoczi, G., Papagrigoriou, E., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.212 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human glycerol-3-phosphate dehydrogenase 1-like protein.

Uppenberg, J., Smee, C., Hozjan, V., Kavanagh, K., Bunkoczi, G., Papagrigoriou, E., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Oppermann, U.

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)

Macromolecule Content 

• Total Structure Weight: 78.1 kDa 
• Atom Count: 5,409 
• Modeled Residue Count: 686 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol-3-phosphate dehydrogenase 1-like protein	A, B	349	Homo sapiens	Mutation(s): 0  Gene Names: GPD1L EC: 1.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N335 (Homo sapiens) Explore Q8N335  Go to UniProtKB:  Q8N335
PHAROS:  Q8N335 GTEx:  ENSG00000152642

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4	C [auth A], D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.212 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.1	α = 90
b = 139.1	β = 90
c = 109.62	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Uppenberg, J., Smee, C., Hozjan, V., Kavanagh, K., Bunkoczi, G., Papagrigoriou, E., Pike, A.C.W., Ugochukwu, E., Umeano, C., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description