8ZHY | pdb_00008zhy

Magnesium substituted Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with CO2.

PDB DOI: https://doi.org/10.2210/pdb8ZHY/pdb

Classification: LYASE
Organism(s): Comamonas testosteroni KF-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-11 Released: 2024-09-25
Deposition Author(s): Kumar, K.A., Pahwa, D., Kumar, P.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.330 (Depositor), 0.332 (DCC)
R-Value Work:
0.283 (Depositor), 0.284 (DCC)

Starting Model: in silico
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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

Magnesium substituted Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with CO2.

Kumar, K.A., Pahwa, D.

To be published.

Macromolecule Content

Total Structure Weight: 141.31 kDa
Atom Count: 9,333
Modeled Residue Count: 1,248
Deposited Residue Count: 1,340
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxythreonine-4-phosphate dehydrogenase	A, B, C, D	335	Comamonas testosteroni KF-1	Mutation(s): 0 Gene Names: CtesDRAFT_PD2128 EC: 1.1.1.262
UniProt
Find proteins for B7WRJ7 (Comamonas testosteroni (strain DSM 14576 / KF-1)) Explore B7WRJ7 Go to UniProtKB: B7WRJ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7WRJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth D] SDF format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] mmCIF format, chain H [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C]	H [auth A], O [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth C] Focus chain P [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C]
CO2 (Subject of Investigation/LOI) Query on CO2 Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth C] SDF format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B]	J [auth B], L [auth C], N [auth C]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth C] Interactions & Density Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Q [auth D] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth D]	K [auth B], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain Q [auth D] Interactions & Density Focus chain K [auth B] Focus chain Q [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth D] MOL2 format, chain I [auth A] MOL2 format, chain R [auth D] mmCIF format, chain I [auth A] mmCIF format, chain R [auth D]	I [auth A], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain R [auth D]