3AGM Transferase Transferase Inhibitor date Apr 02, 2010
title Complex Of Pka With The Bisubstrate Protein Kinase Inhibitor
authors A.Pflug, J.Ragozina, A.Uri, D.Bossemeyer, R.A.Engh
compound source
Molecule: Camp-Dependent Protein Kinase Catalytic Subunit A
Chain: A
Synonym: Pka C-Alpha
Ec: 2.7.11.11
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pkaca, Prkaca
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-285b(+)

Molecule: N~2~-{8-Oxo-8-[4-(9h-Purin-6-Yl)Piperazin-1-Yl]Oc Arginyl-D-Arginyl-D-Arginyl-D-Arginyl-D-Arginyl-D-Argininam
Chain: B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 43 21 2
R_factor 0.223 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.520 85.520 99.040 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 69P, A67, DAR, NH2, OCE, SEP, TPO enzyme Transferase E.C.2.7.11.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDiversity of bisubstrate binding modes of adenosine analogue-oligoarginine conjugates in protein kinase a and implications for protein substrate interactions., Pflug A, Rogozina J, Lavogina D, Enkvist E, Uri A, Engh RA, Bossemeyer D, J Mol Biol. 2010 Oct 15;403(1):66-77. Epub 2010 Aug 21. PMID:20732331
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (3agm.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 3AGM
  • CSU: Contacts of Structural Units for 3AGM
  • Structure Factors (376 Kb)
  • Retrieve 3AGM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AGM from S2C, [Save to disk]
  • Re-refined 3agm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AGM 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.
  • Visual 3D analysis of 3AGM
  • 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 3AGM, from MSDmotif at EBI
  • Fold representative 3agm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3agm_A] [3agm] [3agm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AGM: [S_TK_X] [S_TKc ] by SMART
  • Alignments of the sequence of 3AGM with the sequences similar proteins can be viewed for 3AGM's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3AGM
  • Community annotation for 3AGM 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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