4DM9	Hydrolase, Ligase Inhibitor	date	Feb 07, 2012
title	The Crystal Structure Of Ubiquitin Carboxy-Terminal Hydrolas (Uchl1) Bound To A Tripeptide Fluoromethyl Ketone Z-Vae(Ome
authors	C.W.Davies, J.Chaney, G.Korbel, D.Ringe, G.A.Petsko, H.Ploegh, C.D
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase Isozyme L1 Chain: A, B Synonym: Uch-L1, Neuron Cytoplasmic Protein 9.5, Pgp 9.5, P Ubiquitin Thioesterase L1; Ec: 3.4.19.12, 6.-.-.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Uchl1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-6p1
Molecule: Tripeptide Fluoromethyl Ketone Inhibitor Z-Vae(Om Chain: X, Y Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 4 21 2	R_factor 0.197 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 110.011 110.011 78.745 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.35 Å
ligand	CF0, GME, PHQ	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
Gene Ontology	Chain Function Process Component A, B cysteine-type endopeptidase ... ubiquitin thiolesterase acti... protein binding peptidase activity cysteine-type peptidase acti... omega peptidase activity hydrolase activity ligase activity alpha-2A adrenergic receptor... ubiquitin binding proteolysis ubiquitin-dependent protein ... response to stress axonogenesis axon target recognition adult walking behavior cell death cell proliferation protein deubiquitination sensory perception of pain axon transport of mitochondr... eating behavior negative regulation of MAP k... muscle fiber development neuromuscular process nucleus nucleolus cytoplasm endoplasmic reticulum endoplasmic reticulum membra... cytosol plasma membrane membrane axon neuronal cell body
Primary reference	The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK)., Davies CW, Chaney J, Korbel G, Ringe D, Petsko GA, Ploegh H, Das C, Bioorg Med Chem Lett. 2012 Jun 15;22(12):3900-4. Epub 2012 May 4. PMID:22617491

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk] Biological Unit Coordinates (4dm9.pdb1.gz) 77 Kb Biological Unit Coordinates (4dm9.pdb2.gz) 78 Kb LPC: Ligand-Protein Contacts for 4DM9 CSU: Contacts of Structural Units for 4DM9 Structure Factors (143 Kb) Retrieve 4DM9 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4DM9 from S2C, [Save to disk] Re-refined 4dm9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4DM9 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 4DM9

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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 4DM9, from MSDmotif at EBI Fold representative 4dm9 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4dm9_A] [4dm9_B] [4dm9_X] [4dm9_Y] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 4DM9 with the sequences similar proteins can be viewed for 4DM9'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 4DM9

Community annotation for 4DM9 at PDBWiki (http://pdbwiki.org)

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