3BRV Transferase Transcription date Dec 21, 2007
title Nemoikkb Association Domain Structure
authors L.F.Silvian
compound source
Molecule: Inhibitor Of Nuclear Factor Kappa-B Kinase Subuni
Chain: A, C
Fragment: Nemo-Binding
Synonym: I-Kappa-B-Kinase Beta, Ikbkb, Ikk-Beta, Ikk-B, I-K Kinase 2, Ikk2, Nuclear Factor Nf-Kappa-B Inhibitor Kinase Nfkbikb;
Ec: 2.7.11.10
Engineered: Yes
Synthetic: Yes
Other_details: Peptide Synthesized Corresponds To Residues Of Ikk-Beta Kinase;

Molecule: Nf-Kappa-B Essential Modulator
Chain: B, D
Fragment: Unp Residues 44-111
Synonym: Nemo, Nf-Kappa-B Essential Modifier, Inhibitor Of Factor Kappa-B Kinase Subunit Gamma, Ikb Kinase Subunit Gam Kappa-B Kinase Gamma, Ikk-Gamma, Ikkg, Ikb Kinase-Associate 1, Ikkap1, Fip-3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ikbkg, Fip3, Nemo
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.294
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.820 50.670 102.790 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand
enzyme Transferase E.C.2.7.11.10 BRENDA
Primary referenceStructure of a NEMO/IKK-Associating Domain Reveals Architecture of the Interaction Site., Rushe M, Silvian L, Bixler S, Chen LL, Cheung A, Bowes S, Cuervo H, Berkowitz S, Zheng T, Guckian K, Pellegrini M, Lugovskoy A, Structure. 2008 May;16(5):798-808. PMID:18462684
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (3brv.pdb1.gz) 35 Kb
  • Biological Unit Coordinates (3brv.pdb2.gz) 18 Kb
  • Biological Unit Coordinates (3brv.pdb3.gz) 18 Kb
  • Biological Unit Coordinates (3brv.pdb4.gz) 18 Kb
  • Biological Unit Coordinates (3brv.pdb5.gz) 18 Kb
  • CSU: Contacts of Structural Units for 3BRV
  • Likely Quarternary Molecular Structure file(s) for 3BRV
  • Structure Factors (183 Kb)
  • Retrieve 3BRV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BRV from S2C, [Save to disk]
  • Re-refined 3brv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BRV 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 3BRV
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3BRV, from MSDmotif at EBI
  • Fold representative 3brv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3brv_A] [3brv] [3brv_B] [3brv_D] [3brv_C]
  • SWISS-PROT database: [O14920] [Q9Y6K9]
  • Domain organization of [IKKB_HUMAN] [NEMO_HUMAN] by SWISSPFAM
  • Domain found in 3BRV: [IKKbetaNEMObind ] by SMART
  • Alignments of the sequence of 3BRV with the sequences similar proteins can be viewed for 3BRV's classification [IKKB_HUMAN] [NEMO_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [IKKB_HUMAN] [NEMO_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3BRV
  • Community annotation for 3BRV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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