4GBV

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant A54L with 1,2-ethanediol as Cryo-protectant

PDB DOI: https://doi.org/10.2210/pdb4GBV/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-07-28 Released: 2013-08-21
Deposition Author(s): Honzatko, R.B., Gao, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.243
R-Value Work: 0.177
R-Value Observed: 0.180

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 37.35 kDa
Atom Count: 2,641
Modelled Residue Count: 326
Deposited Residue Count: 335
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase 1	A	335	Sus scrofa	Mutation(s): 1 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
F6P Query on F6P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 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]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.243
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.69	α = 90
b = 82.506	β = 90
c = 166.284	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: 2013-08-21

Deposition Author(s):

Honzatko, R.B.

Gao, Y.

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Structure summary

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4GBV

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant A54L with 1,2-ethanediol as Cryo-protectant

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)