3KVF Hydrolase Signaling Protein date Nov 30, 2009
title Crystal Structure Of The I93m Mutant Of Ubiquitin Carboxy Te Hydrolase L1 Bound To Ubiquitin Vinylmethylester
authors C.W.Davies, T.K.Maiti, C.Das
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase Isozyme L1
Chain: A
Synonym: Uch-L1, Ubiquitin Thioesterase L1, Neuron Cytoplas Protein 9.5, Pgp 9.5, Pgp9.5;
Ec: 3.4.19.12, 6.-.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pgp9.5, Uchl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1

Molecule: Ubiquitin
Chain: B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rps27a, Uba52, Uba80, Ubb, Ubc, Ubcep1, Ubcep2, Ubiq_
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptyb1
symmetry Space Group: H 3 2
R_factor 0.242 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.089 87.089 193.476 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand GVE enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene UBIQ (H. sapiens)
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceUbiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation., Boudreaux DA, Maiti TK, Davies CW, Das C, Proc Natl Acad Sci U S A. 2010 May 18;107(20):9117-22. Epub 2010 May 3. PMID:20439756
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk]
  • Biological Unit Coordinates (3kvf.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 3KVF
  • CSU: Contacts of Structural Units for 3KVF
  • Structure Factors (54 Kb)
  • Retrieve 3KVF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KVF from S2C, [Save to disk]
  • Re-refined 3kvf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KVF 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 3KVF
  • 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 3KVF, from MSDmotif at EBI
  • Fold representative 3kvf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kvf_B] [3kvf_A] [3kvf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KVF: [UBQ ] by SMART
  • Alignments of the sequence of 3KVF with the sequences similar proteins can be viewed for 3KVF's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3KVF
  • Community annotation for 3KVF 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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