4ABF Hydrolase date Dec 08, 2011
title Fragments Bound To Bovine Trypsin For The Sampl Challenge
authors J.Newman, T.S.Peat
compound source
Molecule: Cationic Trypsin
Chain: A
Synonym: Beta-Trypsin, Alpha-Trypsin Chain 1, Alpha-Trypsin
Ec: 3.4.21.4
 Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Pancreas
Other_details: Sigma
symmetry Space Group: P 21 21 21
R_factor 0.144 R_Free 0.161
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.542 58.640 66.494 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand 513, CA, CL, DMS, EDO, SO4 enzyme Hydrolase E.C.3.4.21.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe DINGO dataset: a comprehensive set of data for the SAMPL challenge., Newman J, Dolezal O, Fazio V, Caradoc-Davies T, Peat TS, J Comput Aided Mol Des. 2012 May;26(5):497-503. doi: 10.1007/s10822-011-9521-2., Epub 2011 Dec 21. PMID:22187139
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (4abf.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 4ABF
  • CSU: Contacts of Structural Units for 4ABF
  • Structure Factors (674 Kb)
  • Retrieve 4ABF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ABF from S2C, [Save to disk]
  • Re-refined 4abf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4ABF 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 4ABF
  • 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
  • 3D motif for 4ABF, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4abf_A] [4abf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4ABF: [Tryp_SPc ] by SMART
    • Other resources with information on 4ABF
  • Community annotation for 4ABF at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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