3DCY | pdb_00003dcy

Crystal Structure a TP53-induced glycolysis and apoptosis regulator protein from Homo sapiens.

• PDB DOI: https://doi.org/10.2210/pdb3DCY/pdb

• Classification: apoptosis regulator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-04 Released: 2008-07-15 
• Deposition Author(s): McCoy, J.G., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.229 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal Structure a TP53-induced glycolysis and apoptosis regulator protein from Homo sapiens.

McCoy, J.G., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 31.24 kDa 
• Atom Count: 2,278 
• Modeled Residue Count: 247 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATOR PROTEIN	A	275	Homo sapiens	Mutation(s): 0  Gene Names: C12orf5 EC: 3.1.3.46
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQ88 (Homo sapiens) Explore Q9NQ88  Go to UniProtKB:  Q9NQ88
PHAROS:  Q9NQ88 GTEx:  ENSG00000078237

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.229 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.983	α = 90
b = 76.408	β = 90
c = 79.536	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): McCoy, J.G., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary