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 Diffraction	resolution	1.45 Å
ligand	GVE, MG	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
related structures	by homologous chain: 1UCH, 1YIW
Gene Ontology	Chain Function Process Component A, C ubiquitin thiolesterase acti... peptidase activity cysteine-type peptidase acti... hydrolase activity ubiquitin binding proteolysis ubiquitin-dependent protein ... protein catabolic process intracellular nucleus cytoplasm mitochondrion
Primary reference	Structure 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 (730 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [1xd3_B] [1xd3_C] [1xd3_D] SWISS-PROT database: [P62988] [P15374] Domain organization of [UBIQ_HUMAN] [UCHL3_HUMAN] by SWISSPFAM Domain found in 1XD3: [UBQ ] by SMART Alignments of the sequence of 1XD3 with the sequences similar proteins can be viewed for 1XD3's classification [UBIQ_HUMAN] [UCHL3_HUMAN] 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 [UBIQ_HUMAN] [UCHL3_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1XD3

Community annotation for 1XD3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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