5L8W	Structural Protein	date	Jun 08, 2016
title	Structure Of Usp12-Ub-Prguaf1
authors	S.Dharadhar, T.Sixma
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 12 Chain: A Synonym: Deubiquitinating Enzyme 12,Ubiquitin Thioesterase Ubiquitin-Hydrolyzing Enzyme 1,Ubiquitin-Specific-Processin 12; Ec: 3.4.19.12 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Usp12, Ubh1, Usp12l1 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108
Molecule: Wd Repeat-Containing Protein 48 Chain: B Synonym: Usp1-Associated Factor 1,Wd Repeat Endosomal Prote Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Wdr48, Kiaa1449, Uaf1 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108
Molecule: Polyubiquitin-B Chain: C Engineered: Yes Other_details: Recombinant Expression Followed By Chemical		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubb Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: I 2 2 2	R_factor 0.208 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 103.679 152.820 182.932 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.79 Å
ligand	AYE, GOL, ZN	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme., Dharadhar S, Clerici M, van Dijk WJ, Fish A, Sixma TK, J Struct Biol. 2016 Sep 17. pii: S1047-8477(16)30200-3. doi:, 10.1016/j.jsb.2016.09.011. PMID:27650958

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (223 Kb) [Save to disk] Biological Unit Coordinates (5l8w.pdb1.gz) 216 Kb LPC: Ligand-Protein Contacts for 5L8W CSU: Contacts of Structural Units for 5L8W Structure Factors (2320 Kb) Retrieve 5L8W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5L8W from S2C, [Save to disk] Re-refined 5l8w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5L8W 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 5L8W

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5l8w_A] [5l8w] [5l8w_B] [5l8w_C] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5L8W: [UBQ] [WD40 ] by SMART

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