8Z75

The structure of non-activated thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH)

PDB DOI: https://doi.org/10.2210/pdb8Z75/pdb

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

Deposited: 2024-04-19 Released: 2024-05-08
Deposition Author(s): Varfolomeeva, L.A., Solovieva, A.Y., Shipkov, N.S., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.196
R-Value Work: 0.167
R-Value Observed: 0.168

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

The structure of non-activated thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH)

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

To be published.

Macromolecule Content

Total Structure Weight: 163.3 kDa
Atom Count: 12,307
Modelled Residue Count: 1,390
Deposited Residue Count: 1,467
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine translocation signal domain-containing protein	A, B, C	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C]	P [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C]	G [auth A], M [auth B], T [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain T [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C]	D [auth A] E [auth A] H [auth B] I [auth B] J [auth B] D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], Q [auth C], R [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C]	F [auth A], L [auth B], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C]