OCA Atlas for 3CQW

3CQW

Transferase

date

Apr 03, 2008

title

Crystal Structure Of Akt-1 Complexed With Substrate Peptide And Inhibitor

authors

J.Pandit

compound

source

Molecule: Rac-Alpha Serinethreonine-Protein Kinase
Chain: A
Fragment: Kinase And Agc-Kinase C-Terminal Domains
Synonym: Rac-Pk-Alpha, Protein Kinase B, Pkb, C-Akt
Ec: 2.7.11.1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Gene: Akt1, Pkb, Rac
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_strain: Sf9
Expression_system_vector_type: Baculovirus

Molecule: Glycogen Synthase Kinase-3 Beta
Chain: C
Fragment: Residues 3-12
Synonym: Gsk-3 Beta
Ec: 2.7.11.26
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Is Naturally Found In Homo Sapiens.

symmetry

Space Group: P 1 21 1

R_factor

0.200

R_Free

0.257

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
42.505	55.879	92.864	90.00	102.36	90.00

method

X-Ray Diffraction

resolution

2.00 Å

ligand

CQW, MN, TPO BindingDB

enzyme

Transferase E.C.2.7.11.1 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A	nucleotide binding protein kinase activity protein serine/threonine kin... protein kinase C binding protein binding ATP binding phosphatidylinositol-3,4,5-t... kinase activity transferase activity enzyme binding protein kinase binding nitric-oxide synthase regula... identical protein binding phosphatidylinositol-3,4-bis... 14-3-3 protein binding	protein import into nucleus,... osteoblast differentiation maternal placenta developmen... positive regulation of prote... carbohydrate metabolic proce... glycogen metabolic process glycogen biosynthetic proces... regulation of glycogen biosy... glucose metabolic process translation regulation of translation cellular protein modificatio... protein phosphorylation negative regulation of prote... nitric oxide biosynthetic pr... transport apoptotic process activation-induced cell deat... inflammatory response signal transduction epidermal growth factor rece... G-protein coupled receptor s... multicellular organismal dev... germ cell development nervous system development aging blood coagulation cell proliferation insulin receptor signaling p... fibroblast growth factor rec... apoptotic mitochondrial chan... carbohydrate transport response to heat response to hormone stimulus... gene expression negative regulation of autop... negative regulation of plasm... positive regulation of sodiu... positive regulation of gluco... negative regulation of endop... regulation of neuron project... glucose transport cellular membrane organizati... RNA metabolic process mRNA metabolic process phosphorylation protein ubiquitination peptidyl-serine phosphorylat... cell projection organization... cell differentiation protein catabolic process platelet activation positive regulation of cell ... regulation of cell migration... endocrine pancreas developme... T cell costimulation positive regulation of cycli... negative regulation of fatty... response to food positive regulation of cellu... peripheral nervous system my... positive regulation of prote... cellular response to insulin... regulation of protein locali... positive regulation of pepti... response to fluid shear stre... intracellular signal transdu... glucose homeostasis anagen positive regulation of apopt... negative regulation of apopt... negative regulation of cyste... protein kinase B signaling c... positive regulation of blood... small molecule metabolic pro... innate immune response positive regulation of nitri... positive regulation of fat c... positive regulation of glyco... positive regulation of anti-... negative regulation of cell ... negative regulation of prote... positive regulation of vasoc... positive regulation of trans... nitric oxide metabolic proce... positive regulation of gluco... negative regulation of JNK c... protein autophosphorylation positive regulation of lipid... insulin-like growth factor r... neurotrophin TRK receptor si... phosphatidylinositol-mediate... regulation of nitric-oxide s... positive regulation of nitri... positive regulation of seque... striated muscle cell differe... mammary gland epithelial cel... glycogen cell differentiatio... labyrinthine layer blood ves... response to UV-A cellular response to growth ... cellular response to epiderm... cellular response to hypoxia... positive regulation of estab... negative regulation of relea... intrinsic apoptotic signalin... positive regulation of prote... regulation of cell cycle che...	nucleus nucleoplasm cytoplasm spindle cytosol plasma membrane microtubule cytoskeleton membrane lamellipodium
C	nucleotide binding RNA polymerase II transcript... p53 binding protein kinase activity protein serine/threonine kin... integrin binding protein binding ATP binding beta-catenin binding kinase activity transferase activity transferase activity, transf... protein kinase binding ubiquitin protein ligase bin... protein kinase A catalytic s... ionotropic glutamate recepto... tau protein binding tau-protein kinase activity NF-kappaB binding	re-entry into mitotic cell c... epithelial to mesenchymal tr... positive regulation of cell-... carbohydrate metabolic proce... glycogen metabolic process regulation of gene expressio... protein phosphorylation protein export from nucleus response to stress ER overload response establishment or maintenance... epidermal growth factor rece... multicellular organismal dev... nervous system development axonogenesis axon guidance myoblast fusion circadian rhythm fibroblast growth factor rec... organ morphogenesis negative regulation of signa... response to lithium ion positive regulation of pepti... myotube differentiation Wnt receptor signaling pathw... phosphorylation cell migration peptidyl-serine phosphorylat... hippocampus development establishment of cell polari... cell differentiation negative regulation of prote... positive regulation of prote... negative regulation of prote... positive regulation of prote... positive regulation of Rac G... regulation of microtubule-ba... positive regulation of pepti... protein localization to micr... intracellular signal transdu... response to drug negative regulation of apopt... negative regulation of MAP k... hypermethylation of CpG isla... canonical Wnt receptor signa... innate immune response fat cell differentiation negative regulation of glyco... positive regulation of prote... negative regulation of trans... positive regulation of trans... positive regulation of prote... neurotrophin TRK receptor si... phosphatidylinositol-mediate... regulation of neuronal synap... negative regulation of dendr... negative regulation of NFAT ... canonical Wnt receptor signa... superior temporal gyrus deve... negative regulation of canon... negative regulation of type ... negative regulation of glyco... positive regulation of stem ...	nucleus nucleolus cytoplasm centrosome cytosol plasma membrane membrane growth cone ribonucleoprotein complex beta-catenin destruction com... neuronal cell body dendritic spine dendritic shaft membrane-bounded organelle protein complex membrane raft perinuclear region of cytopl...

Primary reference

Synthesis and structure based optimization of novel Akt inhibitors., Lippa B, Pan G, Corbett M, Li C, Kauffman GS, Pandit J, Robinson S, Wei L, Kozina E, Marr ES, Borzillo G, Knauth E, Barbacci-Tobin EG, Vincent P, Troutman M, Baker D, Rajamohan F, Kakar S, Clark T, Morris J, Bioorg Med Chem Lett. 2008 Apr 15;. PMID:18456494

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]

Biological Unit Coordinates (3cqw.pdb1.gz) 60 Kb

LPC: Ligand-Protein Contacts for 3CQW

CSU: Contacts of Structural Units for 3CQW

Likely Quarternary Molecular Structure file(s) for 3CQW

Structure Factors (1262 Kb)

Retrieve 3CQW in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3CQW from S2C, [Save to disk]

Re-refined 3cqw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3CQW in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3CQW

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

3D motif for 3CQW, from MSDmotif at EBI

Fold representative 3cqw from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3cqw_A] [3cqw_C]

SWISS-PROT database: [P31749] [P49841]

Domain organization of [AKT1_HUMAN] [GSK3B_HUMAN] by SWISSPFAM

Domains found in 3CQW: [S_TK_X] [S_TKc ] by SMART

Alignments of the sequence of 3CQW with the sequences similar proteins can be viewed for 3CQW's classification [AKT1_HUMAN] [GSK3B_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.

A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [AKT1_HUMAN] [GSK3B_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3CQW

Community annotation for 3CQW at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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