3TMP	Hydrolase Protein Binding	date	Aug 31, 2011
title	The Catalytic Domain Of Human Deubiquitinase Duba In Complex Ubiquitin Aldehyde
authors	X.Ma, J.Yin, S.Hymowitz, M.Starovasnik, A.Cochran
compound		source
Molecule: Otu Domain-Containing Protein 5 Chain: A, C, E, G Fragment: Catalytic Or Otu Domain (Residues 172-351) Synonym: Deubiquitinating Enzyme A, Duba Ec: 3.4.19.12 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Duba, Otud5 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21-Codonplus (De3)-Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28b
Molecule: Polyubiquitin-C Chain: B, D, F, H Fragment: Ubiquitin-Like 1 Synonym: Ubiquitin Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubc, Ubiquitin Aldehyde Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 1	R_factor 0.190 R_Free 0.227
crystal cell	length a length b length c angle alpha angle beta angle gamma 59.532 65.296 65.843 90.26 93.53 99.28
method	X-Ray Diffraction	resolution	1.91 Å
ligand	GLZ, SEP	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
note	3TMP is a representative structure
Gene Ontology	Chain Function Process Component A, C, G, E
Primary reference	Phosphorylation-dependent activity of the deubiquitinase DUBA., Huang OW, Ma X, Yin J, Flinders J, Maurer T, Kayagaki N, Phung Q, Bosanac I, Arnott D, Dixit VM, Hymowitz SG, Starovasnik MA, Cochran AG, Nat Struct Mol Biol. 2012 Jan 15;19(2):171-5. doi: 10.1038/nsmb.2206. PMID:22245969

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (181 Kb) [Save to disk] Biological Unit Coordinates (3tmp.pdb1.gz) 46 Kb Biological Unit Coordinates (3tmp.pdb2.gz) 46 Kb Biological Unit Coordinates (3tmp.pdb3.gz) 47 Kb Biological Unit Coordinates (3tmp.pdb4.gz) 45 Kb LPC: Ligand-Protein Contacts for 3TMP CSU: Contacts of Structural Units for 3TMP Structure Factors (993 Kb) Retrieve 3TMP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3TMP from S2C, [Save to disk] Re-refined 3tmp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3TMP 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 3TMP

VIPERdb: visual, structural and computational analysis of 3TMP 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 3D motif for 3TMP, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3tmp_G] [3tmp_H] [3tmp_C] [3tmp_E] [3tmp] [3tmp_D] [3tmp_B] [3tmp_F] [3tmp_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3TMP: [UBQ ] by SMART

Other resources with information on 3TMP

Community annotation for 3TMP at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---