5ZBU	Endocytosis	date	Feb 12, 2018
title	Crystal Structure Of Pa-Tm-Ring E3 Ligase Rnf13 Ring Domain With E2~Ub
authors	A.B.Datta, S.Sarkar
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2 D2 Chain: C, B Synonym: (E3-Independent) E2 Ubiquitin-Conjugating Enzyme D Ubiquitin-Conjugating Enzyme D2,Ubiquitin Carrier Protein D Ubiquitin-Conjugating Enzyme E2(17)Kb 2,Ubiquitin-Conjugati E2-17 Kda 2,Ubiquitin-Protein Ligase D2,P53-Regulated Ubiqu Conjugating Enzyme 1; Ec: 2.3.2.23,2.3.2.24 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ube2d2, Pubc1, Ubc4, Ubc5b, Ubch4, Ubch5b Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta 2 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Petsumo2
Molecule: E3 Ubiquitin-Protein Ligase Rnf13 Chain: A, D Synonym: Ring Finger Protein 13,Ring-Type E3 Ubiquitin Tran Rnf13; Ec: 2.3.2.27 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rnf13, Rzf Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta 2 (De3) Expression_system_plasmid: Petsumo2
Molecule: Ubiquitin Chain: E Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta 2(De3)
symmetry	Space Group: P 1 21 1	R_factor 0.214 R_Free 0.262
crystal cell	length a length b length c angle alpha angle beta angle gamma 56.559 105.740 60.790 90.00 115.49 90.00
method	X-Ray Diffraction	resolution	3.20 Å
ligand	ZN	enzyme	Transferase E.C.2.3.2.23 BRENDA
Gene Ontology	Chain Function Process Component C, B

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk] Biological Unit Coordinates (5zbu.pdb1.gz) 76 Kb Biological Unit Coordinates (5zbu.pdb2.gz) 103 Kb LPC: Ligand-Protein Contacts for 5ZBU CSU: Contacts of Structural Units for 5ZBU Structure Factors (463 Kb) Retrieve 5ZBU in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5ZBU from S2C, [Save to disk]

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Visual 3D analysis of 5ZBU

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5zbu_E] [5zbu_B] [5zbu_D] [5zbu_C] [5zbu_A] SWISS-PROT database: Domain organization of by SWISSPFAM

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