8AGS | pdb_00008ags

Cyclohexane epoxide soak of epoxide hydrolase from metagenomic source ch65 resulting in halogenated compound in the active site

PDB DOI: https://doi.org/10.2210/pdb8AGS/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-07-20 Released: 2023-08-16
Deposition Author(s): Isupov, M.N., De Rose, S.A., Mitchell, D., Littlechild, J.A.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Complexes of epoxide hydrolase from metagenomic source ch65

Isupov, M.N., De Rose, S.A., Mitchell, D., Littlechild, J.A., Parker, E., Ferrandi, E., Guazzelli, E., Monti, D.

To be published.

Macromolecule Content

Total Structure Weight: 71.2 kDa
Atom Count: 5,661
Modeled Residue Count: 586
Deposited Residue Count: 598
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta epoxide hydrolase	A [auth AAA], B [auth BBB]	299	metagenome	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain M [auth BBB] MOL2 format, chain M [auth BBB] mmCIF format, chain M [auth BBB]	M [auth BBB]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain M [auth BBB] Interactions & Density Focus chain M [auth BBB]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Interactions & Density Focus chain E [auth AAA]
2CH (Subject of Investigation/LOI) Query on 2CH Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain N [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain N [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain N [auth BBB]	C [auth AAA], N [auth BBB]	2-CHLOROPHENOL C₆ H₅ Cl O ISPYQTSUDJAMAB-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain N [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain N [auth BBB]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain J [auth AAA] SDF format, chain O [auth BBB] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain I [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain I [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain O [auth BBB] mmCIF format, chain P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain I [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA] F [auth AAA] G [auth AAA] H [auth AAA] I [auth AAA] D [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], O [auth BBB], P [auth BBB], Q [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA]	K [auth AAA], L [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth AAA] Focus chain L [auth AAA] Interactions & Density Focus chain K [auth AAA] Focus chain L [auth AAA]