3G2J

Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in complex with glycogen phosphorylase

PDB DOI: https://doi.org/10.2210/pdb3G2J/pdb

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

Deposited: 2009-01-31 Released: 2010-02-16
Deposition Author(s): Chrysina, E.D., Bokor, E., Alexacou, K.-M., Charavgi, M.-D., Oikonomakos, G.N., Zographos, S.E., Leonidas, D.D., Oikonomakos, N.G., Somsak, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.225
R-Value Work: 0.193
R-Value Observed: 0.195

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Amide-1,2,3-triazole bioisosterism: the glycogen phosphorylase case

Chrysina, E.D., Bokor, E., Alexacou, K.-M., Charavgi, M.-D., Oikonomakos, G.N., Zographos, S.E., Leonidas, D.D., Oikonomakos, N.G., Somsak, L.

(2009) Tetrahedron Asymmetry 20: 733-740

DOI: https://doi.org/10.1016/j.tetasy.2009.03.021

Macromolecule Content

Total Structure Weight: 97.76 kDa
Atom Count: 6,848
Modelled Residue Count: 810
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9GP Query on 9GP 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-(hydroxyacetyl)-beta-D-glucopyranosylamine C₈ H₁₅ N O₇ DIGPTJYOVRRBRM-RHROMQPHSA-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

Binding Affinity Annotations
ID	Source	Binding Affinity
9GP	BindingDB: 3G2J	Ki: min: 1.80e+4, max: 2.00e+4 (nM) from 2 assay(s)
9GP	PDBBind: 3G2J	Ki: 1.79e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.225
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.191	α = 90
b = 127.191	β = 90
c = 115.275	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2023-11-22
Changes: Data collection