8JY1 | pdb_00008jy1

Structure of Mangifera Indica Epoxide hydrolase 2

PDB DOI: https://doi.org/10.2210/pdb8JY1/pdb

Classification: PLANT PROTEIN
Organism(s): Mangifera indica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-02 Released: 2024-08-07
Deposition Author(s): Bhoite, A.S., Gupta, V.S., Kulkarni, K.A.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of Mangifera Indica Epoxide hydrolase 2

Bhoite, A.S., Gupta, V.S., Kulkarni, K.A.

To be published.

Macromolecule Content

Total Structure Weight: 73.6 kDa
Atom Count: 4,634
Modeled Residue Count: 546
Deposited Residue Count: 648
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase-2	A, B	324	Mangifera indica	Mutation(s): 0 Gene Names: EH2 EC: 3.3.2.10
UniProt
Find proteins for A0A1U9ZCB5 (Mangifera indica) Explore A0A1U9ZCB5 Go to UniProtKB: A0A1U9ZCB5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1U9ZCB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.04	α = 90
b = 99.04	β = 90
c = 172.784	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	--

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.