4XCS | pdb_00004xcs

Human peroxiredoxin-1 C83S mutant

• PDB DOI: https://doi.org/10.2210/pdb4XCS/pdb

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


• Deposited: 2014-12-18 Released: 2016-01-13 
• Deposition Author(s): Cho, K.J., Lee, J.-H., Khan, T.G., Park, Y., Cho, A., Chang, T.-S., Kim, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Dimeric Human Peroxiredoxin-1 C83S Mutant

Cho, K.J., Park, Y., Khan, T.G., Lee, J.-H., Kim, S., Seok, J.H., Chung, Y.B., Cho, A.E., Choi, Y., Chang, T.-S., Kim, K.H.

(2015) Bull Korean Chem Soc 36: 1543-1545

• DOI: https://doi.org/10.1002/bkcs.10284

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 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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 147.89 kDa 
• Atom Count: 8,912 
• Modelled Residue Count: 1,066 
• Deposited Residue Count: 1,314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-1	A, B, C, D, E, F	219	Homo sapiens	Mutation(s): 1  Gene Names: PRDX1, PAGA, PAGB, TDPX2 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens) Explore Q06830  Go to UniProtKB:  Q06830
PHAROS:  Q06830 GTEx:  ENSG00000117450

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPS	H [auth A], J [auth D], K [auth E]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
GOL	G [auth A], I [auth C], L [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.788	α = 90
b = 80.128	β = 89.99
c = 125.618	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Cho, K.J., Lee, J.-H., Khan, T.G., Park, Y., Cho, A., Chang, T.-S., Kim, K.H.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-10-05
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary