9QYZ | pdb_00009qyz

MINPP1 from Bacteroides thetaiotaomicron A31Y mutant

PDB DOI: https://doi.org/10.2210/pdb9QYZ/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-04-22 Released: 2025-05-07
Deposition Author(s): Li, A.W.H., Shang, X.Y., Hemmings, A.M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.183 (Depositor), 0.183 (DCC)
R-Value Work:
0.152 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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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

A Structural Basis for the Stereospecificity of Multiple Inositol Polyphosphate Phosphatases

Salmon, M., Shang, X.Y., Li, A.W.H., Hemmings, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 99.21 kDa
Atom Count: 7,173
Modeled Residue Count: 795
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multiple inositol polyphosphate phosphatase 1	A, B	426	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1 Gene Names: BT_4744 EC: 3.1.3.62 (PDB Primary Data), 3.1.3.80 (PDB Primary Data)
UniProt
Find proteins for Q89YI8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89YI8 Go to UniProtKB: Q89YI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89YI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]