3KZZ | pdb_00003kzz

Crystal structure of SNAP-tag bound to its substrate benzylguanine

• PDB DOI: https://doi.org/10.2210/pdb3KZZ/pdb

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


• Deposited: 2009-12-09 Released: 2010-12-15 
• Deposition Author(s): Schmitt, S., Pojer, F., Schiltz, M., Johnsson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

SNAP-tag structure

Schmitt, S., Mollwitz, B., Pojer, F., Bannwarth, M., Schiltz, M., Johnsson, K.

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: 19.71 kDa 
• Atom Count: 1,363 
• Modeled Residue Count: 158 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SNAP-tag	A	182	Homo sapiens	Mutation(s): 0  EC: 2.1.1.63

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OBG	C [auth A]	6-(benzyloxy)-9H-purin-2-amine C12 H11 N5 O KRWMERLEINMZFT-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OBG	BindingDB:  3KZZ	IC50: min: 39, max: 2600 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.16	α = 90
b = 77.16	β = 90
c = 64.81	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Schmitt, S., Pojer, F., Schiltz, M., Johnsson, K.

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description