3IXS	Protein Binding	date	Sep 04, 2009
title	Ring1b C-Terminal Domainrybp C-Terminal Domain Complex
authors	R.Wang, A.B.Taylor, C.A.Kim
compound		source
Molecule: E3 Ubiquitin-Protein Ligase Ring2 Chain: A, C, E, G, I, K Fragment: C-Terminal Domain (Unp Residues 223-333) Synonym: Ring Finger Protein 2, Ring Finger Protein 1b, Rin Finger Protein Bap-1, Ding Protein, Huntingtin-Interacting Interacting Protein 3, Hip2-Interacting Protein 3; Ec: 6.3.2.- Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Bap1, Ding, Hipi3, Ring1b, Rnf2 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-30a
Molecule: Ring1 And Yy1-Binding Protein Chain: B, D, F, H, J, L Fragment: C-Terminal Domain (Unp Residues 145-179) Synonym: Death Effector Domain-Associated Factor, Ded-Assoc Factor, Yy1 And E4tf1-Associated Factor 1, Apoptin-Associat Protein 1, Apap-1; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Dedaf, Rybp, Yeaf1 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-Zl
symmetry	Space Group: P 1	R_factor 0.203 R_Free 0.234
crystal cell	length a length b length c angle alpha angle beta angle gamma 37.894 56.549 100.352 100.88 90.61 100.49
method	X-Ray Diffraction	resolution	1.70 Å
ligand	EDO, NHE	enzyme	Ligase E.C.6.3.2 BRENDA
note	3IXS is a representative structure
Gene Ontology	Chain Function Process Component A, K, E, C, I, G F, J, B, H, D, L
Primary reference	Polycomb group targeting through different binding partners of RING1B C-terminal domain., Wang R, Taylor AB, Leal BZ, Chadwell LV, Ilangovan U, Robinson AK, Schirf V, Hart PJ, Lafer EM, Demeler B, Hinck AP, McEwen DG, Kim CA, Structure. 2010 Aug 11;18(8):966-75. PMID:20696397

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk] Biological Unit Coordinates (3ixs.pdb1.gz) 27 Kb Biological Unit Coordinates (3ixs.pdb2.gz) 29 Kb Biological Unit Coordinates (3ixs.pdb3.gz) 25 Kb Biological Unit Coordinates (3ixs.pdb4.gz) 25 Kb Biological Unit Coordinates (3ixs.pdb5.gz) 23 Kb Biological Unit Coordinates (3ixs.pdb6.gz) 24 Kb LPC: Ligand-Protein Contacts for 3IXS CSU: Contacts of Structural Units for 3IXS Structure Factors (1261 Kb) Retrieve 3IXS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3IXS from S2C, [Save to disk] Re-refined 3ixs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3IXS 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 3IXS

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 3IXS, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ixs_F] [3ixs_D] [3ixs_E] [3ixs_J] [3ixs_I] [3ixs_H] [3ixs_A] [3ixs_C] [3ixs_G] [3ixs_K] [3ixs] [3ixs_L] [3ixs_B] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3IXS

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

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