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
View more details

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
Modelled Residue Count: 318
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 C [auth B] SDF format, chain H [auth A] MOL2 format, chain C [auth B] MOL2 format, chain H [auth A] mmCIF format, chain C [auth B] mmCIF format, chain H [auth A]	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 D [auth B] SDF format, chain I [auth A] MOL2 format, chain D [auth B] MOL2 format, chain I [auth A] mmCIF format, chain D [auth B] mmCIF format, chain I [auth A]	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 E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	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]