1NBF	Hydrolase	date	Dec 02, 2002
title	Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme In And In Complex With Ubiquitin Aldehyde
authors	M.Hu, P.Li, M.Li, W.Li, T.Yao, J.W.Wu, W.Gu, R.E.Cohen, Y.Shi
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 7 Chain: A, B, E Fragment: Hausp Core Domain Synonym: Deubiquitinating Enzyme 7 Ec: 3.1.2.15 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Usp7 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_plasmid: Pgex-2t
Molecule: Ubiquitin Aldehyde Chain: C, D Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Uba52 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.218 R_Free 0.262
crystal cell	length a length b length c angle alpha angle beta angle gamma 99.728 101.166 141.134 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	GLZ	enzyme	Hydrolase E.C.3.1.2.15 BRENDA
related structures	by homologous chain: 1AAR, 1NB8, 1TBE
Gene Ontology	Chain Function Process Component A, E, B
Primary reference	Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde., Hu M, Li P, Li M, Li W, Yao T, Wu JW, Gu W, Cohen RE, Shi Y, Cell 2002 Dec 27;111(7):1041-54. PMID:12507430

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (206 Kb) [Save to disk] Biological Unit Coordinates (1nbf.pdb1.gz) 75 Kb Biological Unit Coordinates (1nbf.pdb2.gz) 74 Kb Biological Unit Coordinates (1nbf.pdb3.gz) 59 Kb LPC: Ligand-Protein Contacts for 1NBF CSU: Contacts of Structural Units for 1NBF Likely Quarternary Molecular Structure file(s) for 1NBF Retrieve 1NBF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1NBF from S2C, [Save to disk]

View 1NBF 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 1NBF

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1NBF, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1nbfa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1nbfb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1nbfc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1nbfd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1nbfe_, region E [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: [1nbf_D] [1nbf_C] [1nbf_B] [1nbf_A] [1nbf_E] [1nbf] SWISS-PROT database: [P62988] [Q93009] Domain organization of [UBIQ_HUMAN] [UBP7_HUMAN] by SWISSPFAM Domain found in 1NBF: [UBQ ] by SMART

Other resources with information on 1NBF

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

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