2I1V

Crystal structure of PFKFB3 in complex with ADP and Fructose-2,6-bisphosphate

PDB DOI: https://doi.org/10.2210/pdb2I1V/pdb

Classification: TRANSFERASE, HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-08-15 Released: 2007-07-03
Deposition Author(s): Kim, S.G., El-Maghrabi, M.R., Lee, Y.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.240

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 60.8 kDa
Atom Count: 3,946
Modelled Residue Count: 449
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	A [auth B]	520	Homo sapiens	Mutation(s): 0 EC: 2.7.1.105 (PDB Primary Data), 3.1.3.46 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16875 (Homo sapiens) Explore Q16875 Go to UniProtKB: Q16875
PHAROS: Q16875 GTEx: ENSG00000170525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16875
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
FDP Query on FDP Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B	B	2,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ YXWOAJXNVLXPMU-ZXXMMSQZSA-N		Interactions Focus chain B Interactions & Density Focus chain B
F6P Query on F6P Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	6-O-phosphono-beta-D-fructofuranose C₆ H₁₃ O₉ P BGWGXPAPYGQALX-ARQDHWQXSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
PHS Query on PHS Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	PHOSPHONIC ACID H₃ O₃ P ABLZXFCXXLZCGV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.240
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.14	α = 90
b = 102.14	β = 90
c = 259.44	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-07-03

Deposition Author(s):

Kim, S.G.

El-Maghrabi, M.R.

Lee, Y.H.

Revision History (Full details and data files)

Version 1.0: 2007-07-03
Type: Initial release
Version 1.1: 2008-04-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary

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2I1V

Crystal structure of PFKFB3 in complex with ADP and Fructose-2,6-bisphosphate

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)