2BKR	Protein-Binding Hydrolase	date	Feb 18, 2005
title	Nedd8 Nedp1 Complex
authors	L.N.Shen, H.Liu, C.Dong, D.Xirodimas, J.H.Naismith, R.T.Hay
compound		source
Molecule: Sentrin-Specific Protease 8 Chain: A Synonym: Nedp1, Sentrinsumo-Specific Protease Senp8, Cyste Protease Fksg8, Protease, Cysteine 2; Ec: 3.4.22.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector: Pet
Molecule: Neddylin Chain: B Synonym: Nedd8, Ubiquitin-Like Protein Nedd8 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector: Pet
symmetry	Space Group: P 21 21 21	R_factor 0.169 R_Free 0.209
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.638 74.226 79.590 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand		enzyme	Hydrolase E.C.3.4.22 BRENDA
note	2BKR is a representative structure
Gene Ontology	Chain Function Process Component A B
Primary reference	Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1., Shen LN, Liu H, Dong C, Xirodimas D, Naismith JH, Hay RT, EMBO J. 2005 Apr 6;24(7):1341-51. Epub 2005 Mar 17. PMID:15775960

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk] Biological Unit Coordinates (2bkr.pdb1.gz) 50 Kb CSU: Contacts of Structural Units for 2BKR Likely Quarternary Molecular Structure file(s) for 2BKR Structure Factors (364 Kb) Retrieve 2BKR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2BKR from S2C, [Save to disk] Re-refined 2bkr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2BKR 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 2BKR

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 2BKR, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2bkr] [2bkr_A] [2bkr_B] SWISS-PROT database: [Q15843] [Q96LD8] Domain organization of [NEDD8_HUMAN] [SENP8_HUMAN] by SWISSPFAM Domain found in 2BKR: [UBQ ] by SMART

Other resources with information on 2BKR

Community annotation for 2BKR at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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