3GZN	Protein Binding Ligase	date	Apr 07, 2009
title	Structure Of Nedd8-Activating Enzyme In Complex With Nedd8 A
authors	M.D.Sintchak
compound		source
Molecule: Nedd8-Activating Enzyme E1 Regulatory Subunit Chain: A, C Synonym: Amyloid Protein-Binding Protein 1, Amyloid Beta Pr Protein-Binding Protein 1, 59 Kda, App-Bp1, Proto-Oncogene Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Appbp1, Hpp1, Nae1 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108 Expression_system_strain: Sf9 Expression_system_vector_type: Baculovirus
Molecule: Nedd8-Activating Enzyme E1 Catalytic Subunit Chain: B, D Synonym: Ubiquitin-Like Modifier-Activating Enzyme 3, Ubiqu Activating Enzyme 3, Nedd8-Activating Enzyme E1c, Ubiquitin Activating Enzyme E1c; Ec: 6.3.2.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Uba3, Ube1c Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108 Expression_system_strain: Sf9 Expression_system_vector_type: Baculovirus
Molecule: Nedd8 Chain: I, J Synonym: Ubiquitin-Like Protein Nedd8, Neddylin, Neural Pre Cell Expressed Developmentally Down-Regulated Protein 8, Ne Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Nedd8 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108 Expression_system_strain: Sf9 Expression_system_vector_type: Baculovirus
symmetry	Space Group: I 2 2 2	R_factor 0.230 R_Free 0.287
crystal cell	length a length b length c angle alpha angle beta angle gamma 135.030 228.715 229.307 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	B39, ZN	enzyme	Ligase E.C.6.3.2 BRENDA
Gene Ontology	Chain Function Process Component A, C D, B J, I
Primary reference	Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ., Brownell JE, Sintchak MD, Gavin JM, Liao H, Bruzzese FJ, Bump NJ, Soucy TA, Milhollen MA, Yang X, Burkhardt AL, Ma J, Loke HK, Lingaraj T, Wu D, Hamman KB, Spelman JJ, Cullis CA, Langston SP, Vyskocil S, Sells TB, Mallender WD, Visiers I, Li P, Claiborne CF, Rolfe M, Bolen JB, Dick LR, Mol Cell. 2010 Jan 15;37(1):102-11. PMID:20129059

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (325 Kb) [Save to disk] Biological Unit Coordinates (3gzn.pdb1.gz) 162 Kb Biological Unit Coordinates (3gzn.pdb2.gz) 161 Kb LPC: Ligand-Protein Contacts for 3GZN CSU: Contacts of Structural Units for 3GZN Structure Factors (1127 Kb) Retrieve 3GZN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GZN from S2C, [Save to disk] Re-refined 3gzn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GZN 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 3GZN

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 3GZN, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gzn] [3gzn_J] [3gzn_C] [3gzn_A] [3gzn_B] [3gzn_D] [3gzn_I] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3GZN: [E2_bind] [UBQ ] by SMART

Other resources with information on 3GZN

Community annotation for 3GZN at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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