8AGM | pdb_00008agm

Limonene epoxide low pH soak of epoxide hydrolase from metagenomic source ch65

PDB DOI: https://doi.org/10.2210/pdb8AGM/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: 1.97 Å
R-Value Free:
0.270 (Depositor), 0.273 (DCC)
R-Value Work:
0.232 (Depositor), 0.235 (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: 141.33 kDa
Atom Count: 10,237
Modeled Residue Count: 1,159
Deposited Residue Count: 1,196
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], C [auth CCC], D [auth DDD]	299	metagenome	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LEO (Subject of Investigation/LOI) Query on LEO Download:Ideal Coordinates CCD File SDF format, chain S [auth DDD] SDF format, chain R [auth DDD] SDF format, chain O [auth CCC] SDF format, chain N [auth CCC] SDF format, chain K [auth BBB] SDF format, chain J [auth BBB] SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain S [auth DDD] MOL2 format, chain R [auth DDD] MOL2 format, chain O [auth CCC] MOL2 format, chain N [auth CCC] MOL2 format, chain K [auth BBB] MOL2 format, chain J [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain S [auth DDD] mmCIF format, chain R [auth DDD] mmCIF format, chain O [auth CCC] mmCIF format, chain N [auth CCC] mmCIF format, chain K [auth BBB] mmCIF format, chain J [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA] F [auth AAA] J [auth BBB] K [auth BBB] N [auth CCC] E [auth AAA], F [auth AAA], J [auth BBB], K [auth BBB], N [auth CCC], O [auth CCC], R [auth DDD], S [auth DDD]	D-LIMONENE 1,2-EPOXIDE C₁₀ H₁₆ O CCEFMUBVSUDRLG-BBBLOLIVSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain N [auth CCC] Focus chain O [auth CCC] Focus chain R [auth DDD] Focus chain S [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain N [auth CCC] Focus chain O [auth CCC] Focus chain R [auth DDD] Focus chain S [auth DDD]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth BBB] MOL2 format, chain I [auth BBB] mmCIF format, chain I [auth BBB]	I [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth BBB] Interactions & Density Focus chain I [auth BBB]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth DDD] SDF format, chain T [auth DDD] SDF format, chain Q [auth CCC] SDF format, chain P [auth CCC] SDF format, chain M [auth BBB] SDF format, chain L [auth BBB] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] MOL2 format, chain U [auth DDD] MOL2 format, chain T [auth DDD] MOL2 format, chain Q [auth CCC] MOL2 format, chain P [auth CCC] MOL2 format, chain M [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain U [auth DDD] mmCIF format, chain T [auth DDD] mmCIF format, chain Q [auth CCC] mmCIF format, chain P [auth CCC] mmCIF format, chain M [auth BBB] mmCIF format, chain L [auth BBB] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA] H [auth AAA] L [auth BBB] M [auth BBB] P [auth CCC] G [auth AAA], H [auth AAA], L [auth BBB], M [auth BBB], P [auth CCC], Q [auth CCC], T [auth DDD], U [auth DDD]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain T [auth DDD] Focus chain U [auth DDD] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain T [auth DDD] Focus chain U [auth DDD]