8AGN | pdb_00008agn

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

PDB DOI: https://doi.org/10.2210/pdb8AGN/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: 1.96 Å
R-Value Free:
0.259 (Depositor), 0.259 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)

Starting Model: experimental
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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: 141.76 kDa
Atom Count: 10,226
Modeled Residue Count: 1,158
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
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain J [auth AAA] SDF format, chain L [auth BBB] SDF format, chain W [auth DDD] SDF format, chain V [auth DDD] MOL2 format, chain G [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain W [auth DDD] MOL2 format, chain V [auth DDD] mmCIF format, chain G [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain W [auth DDD] mmCIF format, chain V [auth DDD]	G [auth AAA], J [auth AAA], L [auth BBB], V [auth DDD], W [auth DDD]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain J [auth AAA] Focus chain L [auth BBB] Focus chain V [auth DDD] Focus chain W [auth DDD] Interactions & Density Focus chain G [auth AAA] Focus chain J [auth AAA] Focus chain L [auth BBB] Focus chain V [auth DDD] Focus chain W [auth DDD]
7EX (Subject of Investigation/LOI) Query on 7EX Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain R [auth CCC] SDF format, chain Y [auth DDD] SDF format, chain X [auth DDD] SDF format, chain Q [auth CCC] SDF format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain R [auth CCC] MOL2 format, chain Y [auth DDD] MOL2 format, chain X [auth DDD] MOL2 format, chain Q [auth CCC] MOL2 format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain M [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain R [auth CCC] mmCIF format, chain Y [auth DDD] mmCIF format, chain X [auth DDD] mmCIF format, chain Q [auth CCC] mmCIF format, chain E [auth AAA]	E [auth AAA] F [auth AAA] M [auth BBB] N [auth BBB] Q [auth CCC] E [auth AAA], F [auth AAA], M [auth BBB], N [auth BBB], Q [auth CCC], R [auth CCC], X [auth DDD], Y [auth DDD]	(1R,6S)-7-oxabicyclo[4.1.0]heptane C₆ H₁₀ O ZWAJLVLEBYIOTI-OLQVQODUSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain Q [auth CCC] Focus chain R [auth CCC] Focus chain X [auth DDD] Focus chain Y [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain Q [auth CCC] Focus chain R [auth CCC] Focus chain X [auth DDD] Focus chain Y [auth DDD]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth DDD] SDF format, chain BA [auth DDD] SDF format, chain K [auth AAA] SDF format, chain P [auth BBB] SDF format, chain S [auth CCC] SDF format, chain U [auth CCC] SDF format, chain Z [auth DDD] SDF format, chain T [auth CCC] SDF format, chain O [auth BBB] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] MOL2 format, chain AA [auth DDD] MOL2 format, chain BA [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain S [auth CCC] MOL2 format, chain U [auth CCC] MOL2 format, chain Z [auth DDD] MOL2 format, chain T [auth CCC] MOL2 format, chain O [auth BBB] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain AA [auth DDD] mmCIF format, chain BA [auth DDD] mmCIF format, chain K [auth AAA] mmCIF format, chain P [auth BBB] mmCIF format, chain S [auth CCC] mmCIF format, chain U [auth CCC] mmCIF format, chain Z [auth DDD] mmCIF format, chain T [auth CCC] mmCIF format, chain O [auth BBB] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA]	AA [auth DDD] BA [auth DDD] H [auth AAA] I [auth AAA] K [auth AAA] AA [auth DDD], BA [auth DDD], H [auth AAA], I [auth AAA], K [auth AAA], O [auth BBB], P [auth BBB], S [auth CCC], T [auth CCC], U [auth CCC], Z [auth DDD]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth DDD] Focus chain BA [auth DDD] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain K [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain Z [auth DDD] Interactions & Density Focus chain AA [auth DDD] Focus chain BA [auth DDD] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain K [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain Z [auth DDD]