4AMX Lyase date Mar 14, 2012
title Crystal Structure Of The Gracilariopsis Lemaneiformis Alpha- Glucan Lyase Covalent Intermediate Complex With 5-Fluoro-Gl Fluoride
authors H.J.Rozeboom, S.Yu, S.Madrid, K.H.Kalk, B.W.Dijkstra
compound source
Molecule: Alpha-1,4-Glucan Lyase Isozyme 1
Chain: A, B, C, D
Fragment: Residues 62-1088
Engineered: Yes
Organism_scientific: Gracilariopsis Lemaneiformis
Organism_taxid: 2782
Expression_system: Ogataea Polymorpha Rb11
Expression_system_taxid: 559303
symmetry Space Group: P 1
R_factor 0.220 R_Free 0.267
length a length b length c angle alpha angle beta angle gamma
91.643 97.008 135.708 80.38 83.11 85.22
method X-Ray Diffractionresolution 2.10 Å
ligand 5GF, AFR, CSO, GOL enzyme Lyase E.C. BRENDA
A, D, C, B

Primary referenceCrystal structure of alpha-1,4-glucan lyase, a unique glycoside hydrolase family member with a novel catalytic mechanism., Rozeboom HJ, Yu S, Madrid S, Kalk KH, Zhang R, Dijkstra BW, J Biol Chem. 2013 Jul 31. PMID:23902768
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1347 Kb) [Save to disk]
  • Biological Unit Coordinates (4amx.pdb1.gz) 344 Kb
  • Biological Unit Coordinates (4amx.pdb2.gz) 341 Kb
  • Biological Unit Coordinates (4amx.pdb3.gz) 339 Kb
  • Biological Unit Coordinates (4amx.pdb4.gz) 343 Kb
  • LPC: Ligand-Protein Contacts for 4AMX
  • CSU: Contacts of Structural Units for 4AMX
  • Structure Factors (11780 Kb)
  • Retrieve 4AMX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AMX from S2C, [Save to disk]
  • Re-refined 4amx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AMX 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 4AMX
  • 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 4AMX, from MSDmotif at EBI
  • Fold representative 4amx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4amx_A] [4amx_D] [4amx] [4amx_C] [4amx_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4AMX
  • Community annotation for 4AMX at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science