9KZ4 | pdb_00009kz4

Dihydrofolate reductase binding to NADPH and trimethoprim-tetramethylrhodamine

PDB DOI: https://doi.org/10.2210/pdb9KZ4/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-09 Released: 2025-01-22
Deposition Author(s): Zhang, K.C., Chen, Z.X.
Funding Organization(s): Chinese Scholarship Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.196 (Depositor), 0.197 (DCC)
R-Value Work:
0.171 (Depositor), 0.177 (DCC)

Starting Model: experimental
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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

Dihydrofolate reductase binding to NADPH and trimethoprim-tetramethylrhodamine

Zhang, K.C., Chen, Z.X.

To be published.

Macromolecule Content

Total Structure Weight: 39.1 kDa
Atom Count: 2,940
Modeled Residue Count: 318
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth B], B [auth A]	159	Escherichia coli K-12	Mutation(s): 0 Gene Names: folA, tmrA, b0048, JW0047 EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4 Go to UniProtKB: P0ABQ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain C [auth B] MOL2 format, chain H [auth A] MOL2 format, chain C [auth B] mmCIF format, chain H [auth A] mmCIF format, chain C [auth B]	C [auth B], H [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth B] Focus chain H [auth A] Interactions & Density Focus chain C [auth B] Focus chain H [auth A]
A1EHX Query on A1EHX Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain D [auth B] MOL2 format, chain I [auth A] MOL2 format, chain D [auth B] mmCIF format, chain I [auth A] mmCIF format, chain D [auth B]	D [auth B], I [auth A]	[9-[5-[2-[4-[[2,4-bis(azanyl)pyrimidin-5-yl]methyl]-2,6-dimethoxy-phenoxy]ethylcarbamoyl]-2-carboxy-phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium C₄₀ H₄₂ N₇ O₇ JYRINKWAGFHPTL-UHFFFAOYSA-O		Interactions Focus chain D [auth B] Focus chain I [auth A] Interactions & Density Focus chain D [auth B] Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] G [auth B] J [auth A] K [auth A] E [auth B], F [auth B], G [auth B], J [auth A], K [auth A], L [auth A], M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]