8Q9Y

The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum in complex with inhibitor thiourea at 1.10 A resolution

PDB DOI: https://doi.org/10.2210/pdb8Q9Y/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pelomicrobium methylotrophicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-22 Released: 2023-09-13
Deposition Author(s): Varfolomeeva, L.A., Polyakov, K.M., Shipkov, N.S., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.125
R-Value Work: 0.107
R-Value Observed: 0.108

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum at atomic resolution

Varfolomeeva, L.A., Polyakov, K.M., Shipkov, N.S., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 109.02 kDa
Atom Count: 8,802
Modelled Residue Count: 938
Deposited Residue Count: 978
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine translocation signal domain-containing protein	A, B	489	Pelomicrobium methylotrophicum	Mutation(s): 0 Gene Names: FR698_09980
UniProt
Find proteins for A0A5C7ETD9 (Pelomicrobium methylotrophicum) Explore A0A5C7ETD9 Go to UniProtKB: A0A5C7ETD9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5C7ETD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
TOU (Subject of Investigation/LOI) Query on TOU Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	THIOUREA C H₄ N₂ S UMGDCJDMYOKAJW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]