6PGV Hydrolase date Jun 24, 2019
title Human Josephin-2 In Complex With Ubiquitin
authors K.C.Grasty, S.D.Weeks, P.J.Loll
compound source
Molecule: Josephin-2
Chain: A
Synonym: Josephin Domain-Containing Protein 2
Ec: 3.4.19.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Josd2, Sbbi54
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pethsul-Jos2

Molecule: Polyubiquitin-B
Chain: B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 61 2 2
R_factor 0.201 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.120 102.120 92.200 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand MSE, NEH enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (6pgv.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 6PGV
  • CSU: Contacts of Structural Units for 6PGV
  • Structure Factors (324 Kb)
  • Retrieve 6PGV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6PGV from S2C, [Save to disk]
  • View 6PGV 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 6PGV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6pgv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6pgv_A] [6pgv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6PGV
  • Community annotation for 6PGV at PDBWiki (http://pdbwiki.org)

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