9GKX

Crystal Structure of Rhizorhabdus wittichii Dimethoate hydrolase (DmhA) in complex with SAHA

PDB DOI: https://doi.org/10.2210/pdb9GKX/pdb

Classification: HYDROLASE
Organism(s): Rhizorhabdus wittichii DC-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-26 Released: 2024-11-06
Deposition Author(s): Graf, L.G., Lammers, M., Schulze, S., Palm, G.J.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.190
R-Value Work: 0.163
R-Value Observed: 0.163

Starting Model: in silico
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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

Distribution and diversity of classical deacylases in bacteria

Graf, L.G., Moreno-Yruela, C., Qin, C., Schulze, S., Palm, G.J., Schmoeker, O., Wang, N., Hocking, D., Jebeli, L., Girbardt, B., Berndt, L., Weis, D.M., Janetzky, M., Zuehlke, D., Sievers, S., Strugnell, R.A., Olsen, C.A., Hofmann, K., Lammers, M.

(2024) Nature Communications

Macromolecule Content

Total Structure Weight: 164.5 kDa
Atom Count: 13,046
Modelled Residue Count: 1,464
Deposited Residue Count: 1,520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimethoate hydrolase	A, B, C, D	380	Rhizorhabdus wittichii DC-6	Mutation(s): 0 Gene Names: dmhA
UniProt
Find proteins for A0A067XIQ6 (Rhizorhabdus wittichii (strain DC-6 / KACC 16600)) Explore A0A067XIQ6 Go to UniProtKB: A0A067XIQ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A067XIQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SHH (Subject of Investigation/LOI) Query on SHH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C]	E [auth A], K [auth C]	OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE C₁₄ H₂₀ N₂ O₃ WAEXFXRVDQXREF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]
OCA Query on OCA Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D]	H [auth B], N [auth D]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain N [auth D] Interactions & Density Focus chain H [auth B] Focus chain N [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]