4GWM Hydrolase date Sep 03, 2012
title Crystal Structure Of Human Promeprin Beta
authors J.L.Arolas, C.Broder, T.Jefferson, T.Guevara, E.E.Sterchi, W.Bode W.Stocker, C.Becker-Pauly, F.X.Gomis-Ruth
compound source
Molecule: Meprin A Subunit Beta
Chain: A, B
Fragment: Promeprin Beta Ectomoiety, Unp Residues 23-614
Synonym: Endopeptidase-2, Meprin B, N-Benzoyl-L-Tyrosyl-P-A Benzoic Acid Hydrolase Subunit Beta, Paba Peptide Hydrolase Beta;
Ec: 3.4.24.63
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mep1b
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1
R_factor 0.168 R_Free 0.188
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.620 71.120 85.740 74.87 80.08 65.13
method X-Ray Diffractionresolution 1.85 Å
ligand BMA, CL, FUC, GOL, MAN, NA, NAG, ZN enzyme Hydrolase E.C.3.4.24.63 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for the sheddase function of human meprin beta metalloproteinase at the plasma membrane., Arolas JL, Broder C, Jefferson T, Guevara T, Sterchi EE, Bode W, Stocker W, Becker-Pauly C, Gomis-Ruth FX, Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16131-6. doi:, 10.1073/pnas.1211076109. Epub 2012 Sep 17. PMID:22988105
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (433 Kb) [Save to disk]
  • Biological Unit Coordinates (4gwm.pdb1.gz) 422 Kb
  • LPC: Ligand-Protein Contacts for 4GWM
  • CSU: Contacts of Structural Units for 4GWM
  • Structure Factors (867 Kb)
  • Retrieve 4GWM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GWM from S2C, [Save to disk]
  • Re-refined 4gwm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GWM 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 4GWM
  • 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 4GWM, from MSDmotif at EBI
  • Fold representative 4gwm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gwm] [4gwm_A] [4gwm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4GWM: [MAM] [MATH] [ZnMc ] by SMART
  • Other resources with information on 4GWM
  • Community annotation for 4GWM at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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