6I33

Crystal structure of human glycine decarboxylase (P-protein)

• PDB DOI: https://doi.org/10.2210/pdb6I33/pdb

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


• Deposited: 2018-11-05 Released: 2019-11-20 
• Deposition Author(s): Van Laer, B., Kapp, U., Leonard, G., Mueller-Dieckmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structural insights in human glycine decarboxylase and comparison with the Neanderthal variant

Van Laer, B., Kapp, U., Signor, L., Leonard, G., Mueller-Dieckmann, C.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 220.14 kDa 
• Atom Count: 14,852 
• Modelled Residue Count: 1,875 
• Deposited Residue Count: 1,968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine dehydrogenase (decarboxylating), mitochondrial	A, B	984	Homo sapiens	Mutation(s): 0  Gene Names: GLDC, GCSP EC: 1.4.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23378 (Homo sapiens) Explore P23378  Go to UniProtKB:  P23378
PHAROS:  P23378 GTEx:  ENSG00000178445

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	C [auth A], J [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT	I [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.81	α = 90
b = 123.51	β = 97.87
c = 99.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Van Laer, B., Kapp, U., Leonard, G., Mueller-Dieckmann, C.

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Advisory, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description