5ZWR | pdb_00005zwr

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.178 (Depositor), 0.179 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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	3D Interactions
9KL Query on 9KL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain D [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth B]	D [auth B], F [auth A]	(2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid C₁₆ H₁₄ O₃ DKYWVDODHFEZIM-NSHDSACASA-N		Interactions Focus chain D [auth B] Focus chain F [auth A] Interactions & Density Focus chain D [auth B] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain C [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth B]	C [auth B], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.178 (Depositor), 0.179 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.156 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Revision History (Full details and data files)

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