8PNO

The MgF3(H2O) transition state analog complex of E. coli YihX

PDB DOI: https://doi.org/10.2210/pdb8PNO/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-30 Released: 2024-07-10
Deposition Author(s): Baumann, P., Zappala, D., Jin, Y.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.257
R-Value Work: 0.212
R-Value Observed: 0.214

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The MgF3(H2O)- transition state analog complex of E. coli YihX

Baumann, P., Zappala, D., Jin, Y.

To be published.

Macromolecule Content

Total Structure Weight: 47.48 kDa
Atom Count: 3,539
Modelled Residue Count: 401
Deposited Residue Count: 404
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-D-glucose 1-phosphate phosphatase YihX	A, B	202	Escherichia coli	Mutation(s): 0 Gene Names: yihX, b3885, JW5566 EC: 3.1.3.10
UniProt
Find proteins for P0A8Y3 (Escherichia coli (strain K12)) Explore P0A8Y3 Go to UniProtKB: P0A8Y3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B]	C [auth A], O [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B]
KQB (Subject of Investigation/LOI) Query on KQB Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B]	D [auth A], M [auth B]	trifluoromagnesate monohydrate F₃ Mg O QUJZUQVZXBKESK-UHFFFAOYSA-J		Interactions Focus chain D [auth A] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B]	I [auth A], J [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B]	G [auth A], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B]	K [auth A], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B]	H [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B]