2JLD

Extremely Tight Binding of Ruthenium Complex to Glycogen Synthase Kinase 3

PDB DOI: https://doi.org/10.2210/pdb2JLD/pdb

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

Deposited: 2008-09-08 Released: 2008-12-09
Deposition Author(s): Atilla-Gokcumen, G.E., Pagano, N., Streu, C., Maksimoska, J., Filippakopoulos, P., Knapp, S., Meggers, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.227
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Extremely Tight Binding of a Ruthenium Complex to Glycogen Synthase Kinase 3.

Atilla-Gokcumen, G.E., Pagano, N., Streu, C., Maksimoska, J., Filippakopoulos, P., Knapp, S., Meggers, E.

(2008) Chembiochem 9: 2933

PubMed: 19035373 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cbic.200800489
Primary Citation of Related Structures:
2JLD

Organizational Affiliation

Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, Marburg, Germany.

Macromolecule Content

Total Structure Weight: 95.42 kDa
Atom Count: 5,709
Modelled Residue Count: 706
Deposited Residue Count: 848
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGEN SYNTHASE KINASE-3 BETA	A, B	420	Homo sapiens	Mutation(s): 0 EC: 2.7.11.26
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841 Go to UniProtKB: P49841
PHAROS: P49841 GTEx: ENSG00000082701
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49841
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE (ALA-GLY-GLY-ALA-ALA-ALA-ALA-ALA)	C [auth E]	8	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG1 Query on AG1 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	D [auth A], E [auth B]	RUTHENIUM PYRIDOCARBAZOLE C₂₇ H₁₇ F N₄ O₇ Ru JXIQPKSJUQUSLH-GXYYWVIJSA-M		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
AG1	PDBBind: 2JLD	IC50: 0.04 (nM) from 1 assay(s)
AG1	Binding MOAD: 2JLD	IC50: 0.04 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.227
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.041	α = 90
b = 86.114	β = 90
c = 177.398	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-09

Deposition Author(s):

Atilla-Gokcumen, G.E.

Revision History (Full details and data files)

Version 1.0: 2008-12-09
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-10-09
Changes: Data collection, Other, Source and taxonomy
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description