5ZWR

Structural Basis for the Enantioselectivity of Est-Y29 toward (S)-ketoprofen

• PDB DOI: https://doi.org/10.2210/pdb5ZWR/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-16 Released: 2019-03-13 
• Deposition Author(s): Ngo, D.T., Oh, C., Park, K., Nguyen, L., Byun, H.M., Kim, S., Yoon, S., Ryu, Y., Ryu, B.H., Kim, T.D., Kim, K.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

Structural Basis for the Enantioselectivity of Esterase Est-Y29 toward (S)-Ketoprofen

Ngo, T.D., Oh, C., Mizar, P., Baek, M., Park, K., Nguyen, L., Byeon, H., Yoon, S., Ryu, B.H., Kim, T.D., Yang, J.W., Seok, C., Lee, S.S., Kim, K.K.

(2019) ACS Catal 9: 755-767

• DOI: https://doi.org/10.1021/acscatal.8b02797

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 89.11 kDa 
• Atom Count: 7,191 
• Modelled Residue Count: 776 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Est-Y29	A [auth B], B [auth A]	401	metagenome	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9KL	D [auth B], F [auth A]	(2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid C16 H14 O3 DKYWVDODHFEZIM-NSHDSACASA-N
GOL	C [auth B], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.156 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.251	α = 90
b = 122.251	β = 90
c = 155.824	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Ngo, D.T., Oh, C., Park, K., Nguyen, L., Byun, H.M., Kim, S., Yoon, S., Ryu, Y., Ryu, B.H., Kim, T.D., Kim, K.K.

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description