8AGP | pdb_00008agp

Halogenated product of limonene epoxide turnover by epoxide hydrolase from metagenomic source ch65

PDB DOI: https://doi.org/10.2210/pdb8AGP/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: 1.49 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (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: 71.23 kDa
Atom Count: 5,643
Modeled Residue Count: 584
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M1U (Subject of Investigation/LOI) Query on M1U Download:Ideal Coordinates CCD File SDF format, chain O [auth BBB] SDF format, chain P [auth BBB] SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain P [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain O [auth BBB] mmCIF format, chain P [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA], D [auth AAA], O [auth BBB], P [auth BBB]	(1~{S},2~{S},4~{R})-2-chloranyl-1-methyl-4-prop-1-en-2-yl-cyclohexan-1-ol C₁₀ H₁₇ Cl O DOPWCACTFDDQSY-UTLUCORTSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] SDF format, chain R [auth BBB] SDF format, chain K [auth AAA] SDF format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain R [auth BBB] MOL2 format, chain K [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain R [auth BBB] mmCIF format, chain K [auth AAA] mmCIF format, chain I [auth AAA]	I [auth AAA] J [auth AAA] K [auth AAA] L [auth AAA] M [auth AAA] I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA], R [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain R [auth BBB] Interactions & Density Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain R [auth BBB]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain Q [auth BBB] SDF format, chain H [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain Q [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain Q [auth BBB] mmCIF format, chain H [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], Q [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain Q [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain Q [auth BBB]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain S [auth BBB] SDF format, chain N [auth AAA] MOL2 format, chain S [auth BBB] MOL2 format, chain N [auth AAA] mmCIF format, chain S [auth BBB] mmCIF format, chain N [auth AAA]	N [auth AAA], S [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth AAA] Focus chain S [auth BBB] Interactions & Density Focus chain N [auth AAA] Focus chain S [auth BBB]