3CUT | pdb_00003cut

Crystal structure of glycogen phosphorylase b in complex with N-(-D-glucopyranosyl)-N'-(2-naphthyl)oxamide

PDB DOI: https://doi.org/10.2210/pdb3CUT/pdb

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

Deposited: 2008-04-17 Released: 2009-04-21
Deposition Author(s): Kyritsi, C., Chrysina, E.D., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.220 (Depositor), 0.219 (DCC)
R-Value Work:
0.193 (Depositor), 0.191 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides

Czifrak, K., Kyritsi, C., Felfoldi, N., Dosca, T., Gergely, P., Chrysina, E.D., Siafaka-Kapadai, A., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

To be published.

Macromolecule Content

Total Structure Weight: 97.9 kDa
Atom Count: 6,826
Modeled Residue Count: 813
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	842	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
179 Query on 179 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]	N-[(naphthalen-2-ylamino)(oxo)acetyl]-beta-D-glucopyranosylamine C₁₈ H₂₀ N₂ O₇ WDRIXCWRSIXUDT-VPKNTQAGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.220 (Depositor), 0.219 (DCC)
R-Value Work: 0.193 (Depositor), 0.191 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.712	α = 90
b = 128.712	β = 90
c = 116.819	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-04-21

Deposition Author(s):

Zographos, S.E.

Oikonomakos, N.G.

Revision History (Full details and data files)

Version 1.0: 2009-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection

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