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:, 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
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. BRENDA
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
  • 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_B] [4dm9_Y] [4dm9_A] [4dm9] [4dm9_X]
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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