4H46 | pdb_00004h46

Crystal Structure of AMP complexes of NEM modified Porcine Liver Fructose-1,6-bisphosphatase

PDB DOI: https://doi.org/10.2210/pdb4H46/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-16 Released: 2013-09-18
Deposition Author(s): Gao, Y., Honzatko, R.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.256 (Depositor), 0.250 (DCC)
R-Value Work:
0.194 (Depositor), 0.190 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Fluorescent 2',3'-O-(2,4,6-trinitrophenyl) (TNP)-AMP Is an Active Site Inhibitor for Porcine Liver Fructose-1,6-bisphosphatase Rather Than Allosteric Inhibitor

Gao, Y., Honzatko, R.B.

To be published.

Macromolecule Content

Total Structure Weight: 37.54 kDa
Atom Count: 2,594
Modeled Residue Count: 319
Deposited Residue Count: 337
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-1,6-bisphosphatase 1	A	337	Sus scrofa	Mutation(s): 0 Gene Names: FBP, FBP1 EC: 3.1.3.11
UniProt
Find proteins for P00636 (Sus scrofa) Explore P00636 Go to UniProtKB: P00636
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00636
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 E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
F6P Query on F6P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-O-phosphono-beta-D-fructofuranose C₆ H₁₃ O₉ P BGWGXPAPYGQALX-ARQDHWQXSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NEN Query on NEN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1-ETHYL-PYRROLIDINE-2,5-DIONE C₆ H₉ N O₂ GHAZCVNUKKZTLG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.256 (Depositor), 0.250 (DCC)
R-Value Work: 0.194 (Depositor), 0.190 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.561	α = 90
b = 78.673	β = 90
c = 164.928	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Gao, Y.

Honzatko, R.B.

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-09
Changes: Structure summary