2ZNV Hydrolase Signaling Protein date May 01, 2008
title Crystal Structure Of Human Amsh-Lp Dub Domain In Complex Wit Linked Ubiquitin Dimer
authors Y.Sato, Y.Azusa, A.Yamagata, H.Mimura, X.Wang, M.Yamashita, K.Ooka O.Nureki, K.Iwai, M.Komada, S.Fukai
compound source
Molecule: Amsh-Like Protease
Chain: A, D
Fragment: Mpn Domain, Dub Domain, Unp Residues 264-436
Synonym: Amsh-Lp, Stam-Binding Protein-Like 1
Ec: 3.1.2.15
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcold Gst

Molecule: Ubiquitin
Chain: B, E
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b

Molecule: Ubiquitin
Chain: C, F
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b
symmetry Space Group: P 1 21 1
R_factor 0.184 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.089 97.363 87.894 90.00 97.49 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand EDO, ZN enzyme Hydrolase E.C.3.1.2.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceStructural basis for specific cleavage of Lys 63-linked polyubiquitin chains., Sato Y, Yoshikawa A, Yamagata A, Mimura H, Yamashita M, Ookata K, Nureki O, Iwai K, Komada M, Fukai S, Nature. 2008 Sep 18;455(7211):358-62. Epub 2008 Aug 31. PMID:18758443
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (2znv.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (2znv.pdb2.gz) 16 Kb
  • Biological Unit Coordinates (2znv.pdb3.gz) 16 Kb
  • Biological Unit Coordinates (2znv.pdb4.gz) 32 Kb
  • Biological Unit Coordinates (2znv.pdb5.gz) 16 Kb
  • Biological Unit Coordinates (2znv.pdb6.gz) 14 Kb
  • LPC: Ligand-Protein Contacts for 2ZNV
  • CSU: Contacts of Structural Units for 2ZNV
  • Likely Quarternary Molecular Structure file(s) for 2ZNV
  • Structure Factors (1055 Kb)
  • Retrieve 2ZNV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZNV from S2C, [Save to disk]
  • Re-refined 2znv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZNV 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 2ZNV
  • 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
  • 3D motif for 2ZNV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2znv_F] [2znv_E] [2znv_A] [2znv_D] [2znv_B] [2znv] [2znv_C]
  • SWISS-PROT database: [Q96FJ0] [P62991]
  • Domain organization of [STALP_HUMAN] [UBIQ_MOUSE] by SWISSPFAM
  • Domains found in 2ZNV: [JAB_MPN] [UBQ ] by SMART
  • Other resources with information on 2ZNV
  • Community annotation for 2ZNV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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