7T2Q | pdb_00007t2q

PEGylated Calmodulin-1 (K148U)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7T2Q

This is version 1.2 of the entry. See complete history

Literature

Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine.

Dowman, L.J.Kulkarni, S.S.Alegre-Requena, J.V.Giltrap, A.M.Norman, A.R.Sharma, A.Gallegos, L.C.Mackay, A.S.Welegedara, A.P.Watson, E.E.van Raad, D.Niederacher, G.Huhmann, S.Proschogo, N.Patel, K.Larance, M.Becker, C.F.W.Mackay, J.P.Lakhwani, G.Huber, T.Paton, R.S.Payne, R.J.

(2022) Nat Commun 13: 6885-6885

  • DOI: https://doi.org/10.1038/s41467-022-34530-z
  • Primary Citation Related Structures: 
    7T2Q

  • PubMed Abstract: 

    The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21 st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.


  • Organizational Affiliation
    • School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia.

Macromolecule Content 

  • Total Structure Weight: 17.07 kDa 
  • Atom Count: 1,266 
  • Modeled Residue Count: 147 
  • Deposited Residue Count: 149 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin-1149Homo sapiensMutation(s): 1 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
H [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.051α = 90
b = 56.347β = 90
c = 116.606γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description