7ONF | pdb_00007onf

The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome

PDB DOI: https://doi.org/10.2210/pdb7ONF/pdb

Classification: TRANSFERASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2021-05-25 Released: 2022-04-06
Deposition Author(s): Tsagkarakou, A.S., Koulas, S.M., Kyriakis, E., Drakou, C.E., Leonidas, D.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.161 (Depositor), 0.171 (DCC)
R-Value Work:
0.129 (Depositor), 0.141 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure activity relationship of the binding of p-coumaroyl glucose to glycogen phosphorylase and its effect on hepatic cell metabolic pathways

Tsagkarakou, A.S., Chasapi, S.A., Koulas, S.M., Tsialtas, I., Kyriakis, E., Drakou, C.E., Kun, S., Somsak, L., Spyroulias, G.A., Psarra, A.M.G., Leonidas, D.D.

(2021) Eur J Med Chem Rep 3: 100011

DOI: https://doi.org/10.1016/j.ejmcr.2021.100011

Macromolecule Content

Total Structure Weight: 96.2 kDa
Atom Count: 7,160
Modeled Residue Count: 810
Deposited Residue Count: 825
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	825	Oryctolagus cuniculus	Mutation(s): 0 EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489 Go to UniProtKB: P00489
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMP Query on IMP 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]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
VKK (Subject of Investigation/LOI) Query on VKK 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]	p-coumaroyl glucose C₁₅ H₁₈ O₈ DSNCQKUYZOSARM-QVLXMGEUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PLP Query on PLP 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]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.161 (Depositor), 0.171 (DCC)
R-Value Work: 0.129 (Depositor), 0.141 (DCC)
R-Value Observed: 0.130 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.607	α = 90
b = 128.607	β = 90
c = 116.633	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-04-06

Deposition Author(s):

Tsagkarakou, A.S.

Revision History (Full details and data files)

Version 1.0: 2022-04-06
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.