4AMW Lyase date Mar 14, 2012
title Crystal Structure Of The Gracilariopsis Lemaneiformis Alpha- 1,4-Glucan Lyase Covalent Intermediate Complex With 5- Fluoro-Idosyl-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
Ec: 4.2.2.13
Engineered: Yes
Organism_scientific: Gracilariopsis Lemaneiformis
Organism_taxid: 2782
Expression_system: Pichia Angusta
Expression_system_taxid: 559303
Expression_system_strain: Rb11
symmetry Space Group: P 1
R_factor 0.20665 R_Free 0.25432
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.100 97.300 136.280 80.31 83.29 85.21
method X-Ray Diffractionresolution 1.90 Å
ligand 5DI, B9D, CSO, GOL enzyme Lyase E.C.4.2.2.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (1460 Kb) [Save to disk]
  • Biological Unit Coordinates (4amw.pdb1.gz) 372 Kb
  • Biological Unit Coordinates (4amw.pdb2.gz) 368 Kb
  • Biological Unit Coordinates (4amw.pdb3.gz) 366 Kb
  • Biological Unit Coordinates (4amw.pdb4.gz) 374 Kb
  • LPC: Ligand-Protein Contacts for 4AMW
  • CSU: Contacts of Structural Units for 4AMW
  • Structure Factors (4685 Kb)
  • Retrieve 4AMW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AMW from S2C, [Save to disk]
  • Re-refined 4amw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AMW 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 4AMW
  • 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 4AMW, from MSDmotif at EBI
  • Fold representative 4amw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4amw_D] [4amw_C] [4amw_B] [4amw_A] [4amw]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4AMW
  • Community annotation for 4AMW at PDBWiki (http://pdbwiki.org)

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