2Q8M

T-like Fructose-1,6-bisphosphatase from Escherichia coli with AMP, Glucose 6-phosphate, and Fructose 1,6-bisphosphate bound

PDB DOI: https://doi.org/10.2210/pdb2Q8M/pdb

Classification: HYDROLASE
Organism(s): Shigella boydii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-06-11 Released: 2007-06-19
Deposition Author(s): Hines, J.K., Kruesel, C.E., Fromm, H.J., Honzatko, R.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.235
R-Value Work: 0.209
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 76.16 kDa
Atom Count: 5,305
Modelled Residue Count: 620
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphatase	A, B	332	Shigella boydii	Mutation(s): 6 Gene Names: fbp EC: 3.1.3.11
UniProt
Find proteins for P0A993 (Escherichia coli (strain K12)) Explore P0A993 Go to UniProtKB: P0A993
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A993
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A]	I [auth A], N [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B]	D [auth A], J [auth B]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
BG6 Query on BG6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	6-O-phosphono-beta-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B]	G [auth A], H [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	E [auth A], F [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
AMP	Binding MOAD: 2Q8M	Ki: 9.40e+4 (nM) from 1 assay(s)
AMP	PDBBind: 2Q8M	Ki: 9.40e+4 (nM) from 1 assay(s)
BG6	Binding MOAD: 2Q8M	Ki: 7.00e+5 (nM) from 1 assay(s)
FBP	Binding MOAD: 2Q8M	IC50: 6000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.235
R-Value Work: 0.209
R-Value Observed: 0.212
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.64	α = 90
b = 124.64	β = 90
c = 132.28	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2023-11-15
Changes: Data collection

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Help and Resources

2Q8M

T-like Fructose-1,6-bisphosphatase from Escherichia coli with AMP, Glucose 6-phosphate, and Fructose 1,6-bisphosphate bound

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)