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 Diffractionresolution 2.35 Å
ligand CF0, GME, PHQ enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe 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.
  • Visual 3D analysis of 4DM9
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • 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_B] [4dm9_Y] [4dm9_A] [4dm9] [4dm9_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4DM9
  • Community annotation for 4DM9 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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