5YDK	Signaling Protein	date	Sep 13, 2017
title	Crystal Structure Of Rnf168 Udm1 In Complex With Lys63-Linke Diubiquitin, Tetrameric Form
authors	T.S.Takahashi, Y.Sato, S.Fukai
compound		source
Molecule: E3 Ubiquitin-Protein Ligase Rnf168 Chain: A, G, F, L Fragment: Unp Residues 113-194 Synonym: Hrnf168,Ring Finger Protein 168,Ring-Type E3 Ubiqu Transferase Rnf168; Ec: 2.3.2.27 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rnf168 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin-40s Ribosomal Protein S27a Chain: B, H, E, K Fragment: Unp Residues 1-76 Synonym: Ubiquitin Carboxyl Extension Protein 80 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rps27a, Uba80, Ubcep1 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin-40s Ribosomal Protein S27a Chain: D, J, C, I Fragment: Unp Residues 1-76 Synonym: Ubiquitin Carboxyl Extension Protein 80 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rps27a, Uba80, Ubcep1 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 1 21 1	R_factor 0.230 R_Free 0.260
crystal cell	length a length b length c angle alpha angle beta angle gamma 85.344 64.120 117.464 90.00 109.62 90.00
method	X-Ray Diffraction	resolution	2.51 Å
ligand	GOL	enzyme	Transferase E.C.2.3.2.27 BRENDA
Primary reference	Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168., Takahashi TS, Hirade Y, Toma A, Sato Y, Yamagata A, Goto-Ito S, Tomita A, Nakada S, Fukai S, Nat Commun. 2018 Jan 12;9(1):170. doi: 10.1038/s41467-017-02345-y. PMID:29330428

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk] Biological Unit Coordinates (5ydk.pdb1.gz) 41 Kb Biological Unit Coordinates (5ydk.pdb2.gz) 40 Kb Biological Unit Coordinates (5ydk.pdb3.gz) 41 Kb Biological Unit Coordinates (5ydk.pdb4.gz) 40 Kb LPC: Ligand-Protein Contacts for 5YDK CSU: Contacts of Structural Units for 5YDK Structure Factors (1012 Kb) Retrieve 5YDK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5YDK from S2C, [Save to disk]

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Visual 3D analysis of 5YDK

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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: [5ydk_I] [5ydk_H] [5ydk_J] [5ydk_E] [5ydk_A] [5ydk_C] [5ydk_L] [5ydk_D] [5ydk_F] [5ydk_B] [5ydk_G] [5ydk_K] SWISS-PROT database: Domain organization of by SWISSPFAM

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