1Q5W	Protein Binding	date	Aug 11, 2003
title	Ubiquitin Recognition By Npl4 Zinc-Fingers
authors	S.L.Alam, J.Sun, M.Payne, B.D.Welch, B.K.Blake, D.R.Davis, H.H.Mey S.D.Emr, W.I.Sundquist
compound		source
Molecule: Homolog Of Yeast Nuclear Protein Localization 4 Chain: A Fragment: Npl4 Nzf Domain (Residues 580-608) Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Gene: Npl4 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: T7 Expression_system_plasmid: Pgex2t
Molecule: Ubiquitin Chain: B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: (Uba52 Or Ubcep2) And Ubb And Ubc And (Uba80 Or Ubcep Rps27a); Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: T7 Expression_system_plasmid: Pet3d
method	Solution NMR
ligand	ZN	enzyme
related structures	by homologous chain: 1NJ3
Primary reference	Ubiquitin interactions of NZF zinc fingers., Alam SL, Sun J, Payne M, Welch BD, Blake BK, Davis DR, Meyer HH, Emr SD, Sundquist WI, EMBO J 2004 Apr 7;23(7):1411-21. Epub 2004 Mar 18. PMID:15029239

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (558 Kb) [Save to disk] Biological Unit Coordinates (1q5w.pdb1.gz) 28 Kb LPC: Ligand-Protein Contacts for 1Q5W CSU: Contacts of Structural Units for 1Q5W Experimental data, such as chemical shifts, at BioMagResBank (BMRB) NMR Restraints Grid from BioMagResBank (BMRB) Retrieve 1Q5W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1Q5W from S2C, [Save to disk]

View 1Q5W 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 1Q5W

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1Q5W, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1q5wa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1q5wb_, region B [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: [1q5w_A] [1q5w_B] [1q5w] SWISS-PROT database: [Q9ES54] [P62988] Domain organization of [NPL4_RAT] [UBIQ_HUMAN] by SWISSPFAM Domains found in 1Q5W: [UBQ] [ZnF_RBZ ] by SMART

Other resources with information on 1Q5W

Community annotation for 1Q5W at PDBWiki (http://pdbwiki.org) NMR Ensemble (OLDERADO: core, domain and representative structure database) MMDB (Entrez's Structure Database)

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