1XD3 Hydrolase date Sep 03, 2004
title Crystal Structure Of Uchl3-Ubvme Complex
authors S.Misaghi, P.J.Galardy, W.J.N.Meester, H.Ovaa, H.L.Ploegh, R.Gaudet
compound source
Molecule: Ubiquitin Carboxyl-Terminal Esterase L3
Chain: A, C
Synonym: Uch-L3, Ubiquitin Thiolesterase, Ubiquitin C- Terminal Hydrolase;
Ec: 3.4.19.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prset

Molecule: Ubc Protein
Chain: B, D
Synonym: Ubiquitin Fused To Vinyl Methylester, Ubvme
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptyb
symmetry Space Group: P 1
R_factor 0.166 R_Free 0.192
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.110 49.290 67.620 86.12 75.03 76.78
method X-Ray Diffractionresolution 1.45 Å
ligand GVE, MG enzyme Hydrolase E.C.3.4.19.12 BRENDA
related structures by homologous chain: 1UCH, 1YIW
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate., Misaghi S, Galardy PJ, Meester WJ, Ovaa H, Ploegh HL, Gaudet R, J Biol Chem 2004 Nov 5;. PMID:15531586
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (1xd3.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (1xd3.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 1XD3
  • CSU: Contacts of Structural Units for 1XD3
  • Likely Quarternary Molecular Structure file(s) for 1XD3
  • Structure Factors (779 Kb)
  • Retrieve 1XD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XD3 from S2C, [Save to disk]
  • Re-refined 1xd3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XD3 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 1XD3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1XD3 1XD3A 1XD3B 1XD3C 1XD3D from the CEP Server.
  • 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 1XD3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xd3a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1xd3b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1xd3c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1xd3d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1xd3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xd3_D] [1xd3] [1xd3_C] [1xd3_B] [1xd3_A]
  • SWISS-PROT database: [P62988] [P15374]
  • Domain organization of [UBIQ_HUMAN] [UCHL3_HUMAN] by SWISSPFAM
  • Domain found in 1XD3: [UBQ ] by SMART
  • Other resources with information on 1XD3
  • Community annotation for 1XD3 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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