9KW8 | pdb_00009kw8

Polyether epoxide hydrolase MonBI-MonBII complex with product analogue

PDB DOI: https://doi.org/10.2210/pdb9KW8/pdb

Classification: HYDROLASE
Organism(s): Streptomyces virginiae
Expression System: Escherichia
Mutation(s): No

Deposited: 2024-12-05 Released: 2025-12-10
Deposition Author(s): Yao, M., Dosen, T., Minami, A., Ozaki, T., Maenaka, K., Kumeta, H., Oikawa, H., Ose, T.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free:
0.266 (Depositor), 0.267 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A paring system of polyether epoxide hydrolases enables a mouldable enzyme for consecutive ring cyclisation cascade

Yabuno, N., Minami, A., Ozaki, T., Owada, Y., Sawada, K., Arai, A., Tadokoro, T., Aizawa, T., Dosen, T., Nomai, T., Matsumaru, T., Junyang, L., Tao, Y., Kodama, A., Uchiyama, S., Hengphasatporn, K., Shigeta, Y., Saio, T., Maenaka, K., Yao, M., Kumeta, H., Oikawa, H., Ose, T.

To be published.

Macromolecule Content

Total Structure Weight: 134.78 kDa
Atom Count: 8,452
Modeled Residue Count: 1,082
Deposited Residue Count: 1,208
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MonBI,MonBII	A, B, C, D	302	Streptomyces virginiae	Mutation(s): 0 Gene Names: monBI, monBII
UniProt
Find proteins for Q846W7 (Streptomyces virginiae) Explore Q846W7 Go to UniProtKB: Q846W7
Find proteins for Q846W8 (Streptomyces virginiae) Explore Q846W8 Go to UniProtKB: Q846W8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q846W8Q846W7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L6P (Subject of Investigation/LOI) Query on A1L6P Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	[(2~{S},3~{R})-2-methyl-3-[(2~{S},5~{R})-2-methyl-5-[(2~{S})-2,5,5-trimethyloxolan-2-yl]oxolan-2-yl]-3-oxidanyl-propyl] hexanoate C₂₂ H₄₀ O₅ WEWKCWFBYOEHQB-ZUCBFVJTSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free: 0.266 (Depositor), 0.267 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.92	α = 90
b = 135.008	β = 90
c = 144.516	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H04634
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H01754
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	22K19282