4JJQ Hydrolase date Mar 08, 2013
title Crystal Structure Of Usp7-Ntd With An E2 Enzyme
authors V.Saridakis
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 7
Chain: A
Fragment: Usp7-Ntd, Unp Residues 54-205
Synonym: Deubiquitinating Enzyme 7, Herpesvirus-Associated Specific Protease, Ubiquitin Thioesterase 7, Ubiquitin-Spec Processing Protease 7;
Ec: 3.4.19.12
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hausp, Usp7, Usp7hausp
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Ubiquitin-Conjugating Enzyme E2 E1
Chain: B
Fragment: Unp Residues 5-14
Synonym: Ubch6, Ubiquitin Carrier Protein E1, Ubiquitin-Pro Ligase E1;
Ec: 6.3.2.19
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Synthesized Peptide
symmetry Space Group: P 41
R_factor 0.197 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.901 69.901 45.733 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand
enzyme Hydrolase E.C.3.4.19.12 BRENDA
Primary referenceUbiquitin-specific protease 7 is a regulator of ubiquitin-conjugating enzyme UbE2E1., Sarkari F, Wheaton K, La Delfa A, Mohamed M, Shaikh F, Khatun R, Arrowsmith CH, Frappier L, Saridakis V, Sheng Y, J Biol Chem. 2013 Jun 7;288(23):16975-85. doi: 10.1074/jbc.M113.469262. Epub 2013, Apr 19. PMID:23603909
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (4jjq.pdb1.gz) 25 Kb
  • CSU: Contacts of Structural Units for 4JJQ
  • Structure Factors (113 Kb)
  • Retrieve 4JJQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JJQ from S2C, [Save to disk]
  • Re-refined 4jjq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JJQ 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 4JJQ
  • 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 4JJQ, from MSDmotif at EBI
  • Fold representative 4jjq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jjq_B] [4jjq_A] [4jjq]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4JJQ: [MATH ] by SMART
  • Other resources with information on 4JJQ
  • Community annotation for 4JJQ at PDBWiki (http://pdbwiki.org)

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