9PGZ | pdb_00009pgz

X-ray crystal structure of SRD42

• PDB DOI: https://doi.org/10.2210/pdb9PGZ/pdb

• Classification: TRANSFERASE
• Organism(s): Priestia megaterium, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-08 Released: 2025-12-24 
• Deposition Author(s): Kuzelka, K.P., Nair, S.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Enhancing enzymatic bioconjugation efficiency via installation of a substrate recruitment domain

Shelby, C., Kuzelka, K.P., Ellis, J.M., Yao, Z., McCue, A.C., Park, R., Nair, S.K., Bowers, A., Kuhlman, B.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.52 kDa 
• Atom Count: 2,918 
• Modeled Residue Count: 348 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosinase,Tyrosine-protein kinase Fyn	A	353	Priestia megaterium, Homo sapiens This entity is chimeric	Mutation(s): 0  EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for B2ZB02 (Priestia megaterium) Explore B2ZB02  Go to UniProtKB:  B2ZB02
Find proteins for P06241 (Homo sapiens) Explore P06241  Go to UniProtKB:  P06241
PHAROS:  P06241 GTEx:  ENSG00000010810
UniProt Groups	P06241B2ZB02

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.264	α = 90
b = 150.264	β = 90
c = 150.264	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Kuzelka, K.P., Nair, S.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release