5R9W Transferase date Mar 04, 2020
title Pandda Analysis Group Deposition Form1 Map Kinase P38-Alpha Fragment N13598a In Complex With Map Kinase P38-Alpha
authors G.F.De Nicola, C.E.Nichols
compound source
Molecule: Mitogen-Activated Protein Kinase 14
Chain: A
Synonym: Mapk 14,Crk1,Mitogen-Activated Protein Kinase P38 Kinase P38 Alpha;
Ec: 2.7.11.24
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Mapk14, Crk1, Csbp1, Csbp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.174 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.133 86.441 126.976 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.89 Å
ligand CL, DMS, MG, SO4, STV enzyme Transferase E.C.2.7.11.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1beta-IL1R and p38alpha-TAB1 Complexes., Nichols C, Ng J, Keshu A, Kelly G, Conte MR, Marber MS, Fraternali F, De Nicola GF, J Med Chem. 2020 Jul 1. doi: 10.1021/acs.jmedchem.0c00403. PMID:32543856
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (5r9w.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 5R9W
  • CSU: Contacts of Structural Units for 5R9W
  • Structure Factors (4615 Kb)
  • Retrieve 5R9W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5R9W from S2C, [Save to disk]
  • View 5R9W 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 5R9W
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5r9w_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5R9W
  • Community annotation for 5R9W at PDBWiki (http://pdbwiki.org)

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