8ZJ7 | pdb_00008zj7

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate and NAD.

PDB DOI: https://doi.org/10.2210/pdb8ZJ7/pdb

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

Deposited: 2024-05-14 Released: 2024-09-25
Deposition Author(s): Kumar, K.A., Pahwa, D., Kumar, P.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.252 (Depositor), 0.269 (DCC)
R-Value Work:
0.181 (Depositor)

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

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate and NAD.

Kumar, K.A., Pahwa, D.

To be published.

Macromolecule Content

Total Structure Weight: 134.64 kDa
Atom Count: 9,432
Modeled Residue Count: 1,252
Deposited Residue Count: 1,264
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 [auth B], B [auth C], C [auth D], D [auth A]	316	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain E [auth B] MOL2 format, chain N [auth A] MOL2 format, chain E [auth B] mmCIF format, chain N [auth A] mmCIF format, chain E [auth B]	E [auth B], N [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth B] Focus chain N [auth A] Interactions & Density Focus chain E [auth B] Focus chain N [auth A]
DHB (Subject of Investigation/LOI) Query on DHB Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain J [auth D] SDF format, chain G [auth C] MOL2 format, chain O [auth A] MOL2 format, chain J [auth D] MOL2 format, chain G [auth C] mmCIF format, chain O [auth A] mmCIF format, chain J [auth D] mmCIF format, chain G [auth C]	G [auth C], J [auth D], O [auth A]	3,4-DIHYDROXYBENZOIC ACID C₇ H₆ O₄ YQUVCSBJEUQKSH-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain J [auth D] Focus chain O [auth A] Interactions & Density Focus chain G [auth C] Focus chain J [auth D] Focus chain O [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain K [auth D] SDF format, chain H [auth C] SDF format, chain F [auth B] MOL2 format, chain P [auth A] MOL2 format, chain K [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] mmCIF format, chain P [auth A] mmCIF format, chain K [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B]	F [auth B], H [auth C], K [auth D], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth C] Focus chain K [auth D] Focus chain P [auth A] Interactions & Density Focus chain F [auth B] Focus chain H [auth C] Focus chain K [auth D] Focus chain P [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]