6ECB Hydrolase date Aug 07, 2018
title Vlm2 Thioesterase Domain Wild Type Structure 1
authors D.A.Alonzo, T.M.Schmeing
compound source
Molecule: Vlm2
Chain: A
Fragment: Thioesterase Domain (Unp Residues 2368-2655)
Ec: 3.1.2.-
Engineered: Yes
Organism_scientific: Streptomyces Tsusimaensis
Organism_taxid: 285482
Atcc: 15141
Gene: Vlm2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 4 3 2
R_factor 0.172 R_Free 0.188
length a length b length c angle alpha angle beta angle gamma
151.399 151.399 151.399 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
enzyme Hydrolase E.C.3.1.2 BRENDA

Primary referenceTrapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid., Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW, Nature. 2018 Dec 12. pii: 10.1038/s41586-018-0781-z. doi:, 10.1038/s41586-018-0781-z. PMID:30542153
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (6ecb.pdb1.gz) 129 Kb
  • CSU: Contacts of Structural Units for 6ECB
  • Structure Factors (2269 Kb)
  • Retrieve 6ECB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ECB from S2C, [Save to disk]
  • View 6ECB 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 6ECB
  • 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: [6ecb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6ECB
  • Community annotation for 6ECB at PDBWiki (http://pdbwiki.org)

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