1P3Q	Translation	date	Apr 18, 2003
title	Mechanism Of Ubiquitin Recognition By The Cue Domain Of Vps9
authors	G.Prag, S.Misra, E.A.Jones, R.Ghirlando, B.A.Davies, B.F.Horazdov J.H.Hurley
compound		source
Molecule: Vacuolar Protein Sorting-Associated Protein Vps9 Chain: Q, R Fragment: Cue Domain Synonym: Vps9p Engineered: Yes Mutation: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Gene: Vps9 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: B834 Plys Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-Parallel.His-Cue
Molecule: Ubiquitin Chain: U, V		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913 Tissue: Red Blood Cells
symmetry	Space Group: C 1 2 1	R_factor 0.260 R_Free 0.277
crystal cell	length a length b length c angle alpha angle beta angle gamma 101.607 45.887 57.802 90.00 96.53 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	MSE	enzyme
note	1P3Q is a representative structure
related structures	by homologous chain: 1BT0, 1MN3, 1UBI
Primary reference	Mechanism of ubiquitin recognition by the CUE domain of Vps9p., Prag G, Misra S, Jones EA, Ghirlando R, Davies BA, Horazdovsky BF, Hurley JH, Cell 2003 May 30;113(5):609-20. PMID:12787502

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk] Biological Unit Coordinates (1p3q.pdb1.gz) 27 Kb Biological Unit Coordinates (1p3q.pdb2.gz) 14 Kb LPC: Ligand-Protein Contacts for 1P3Q CSU: Contacts of Structural Units for 1P3Q Likely Quarternary Molecular Structure file(s) for 1P3Q Structure Factors (236 Kb) Retrieve 1P3Q in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1P3Q from S2C, [Save to disk] Re-refined 1p3q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1P3Q 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 1P3Q

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 1P3Q, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1p3qq_, region Q [Jmol] [rasmolscript] [script source]     - Domain d1p3qr_, region R [Jmol] [rasmolscript] [script source]     - Domain d1p3qu_, region U [Jmol] [rasmolscript] [script source]     - Domain d1p3qv_, region V [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1p3q] [1p3q_R] [1p3q_Q] [1p3q_U] [1p3q_V] SWISS-PROT database: [P62990] [P54787] Domain organization of [UBIQ_BOVIN] [VPS9_YEAST] by SWISSPFAM Domains found in 1P3Q: [CUE] [UBQ ] by SMART

Other resources with information on 1P3Q

Community annotation for 1P3Q at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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