1Y6L	Ligase	date	Dec 06, 2004
title	Human Ubiquitin Conjugating Enzyme E2e2
authors	J.R.Walker, G.V.Avvakumov, E.M.Newman, F.Mackenzie, I.Kozieradzk A.Bochkarev, M.Sundstrom, C.Arrowsmith, A.Edwards, S.Dhe-Pagano Structural Genomics Consortium (Sgc)
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2e2 Chain: A, B, C Fragment: Residues 55-201 Synonym: Ubiquitin-Protein Ligase E2, Ubiquitin Carrier Pro Ubch8; Ec: 6.3.2.19 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ube2e2, Ubch8 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: C 1 2 1	R_factor 0.192 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 108.109 36.110 130.568 90.00 99.92 90.00
method	X-Ray Diffraction	resolution	1.85 Å
ligand		enzyme	Ligase E.C.6.3.2.19 BRENDA
related structures	by homologous chain: 1X23, 1Z2U
Primary reference	A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen., Sheng Y, Hong JH, Doherty R, Srikumar T, Shloush J, Avvakumov GV, Walker JR, Xue S, Neculai D, Wan JW, Kim SK, Arrowsmith CH, Raught B, Dhe-Paganon S, Mol Cell Proteomics. 2012 Aug;11(8):329-41. Epub 2012 Apr 10. PMID:22496338

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk] Biological Unit Coordinates (1y6l.pdb1.gz) 26 Kb Biological Unit Coordinates (1y6l.pdb2.gz) 26 Kb Biological Unit Coordinates (1y6l.pdb3.gz) 26 Kb CSU: Contacts of Structural Units for 1Y6L Likely Quarternary Molecular Structure file(s) for 1Y6L Structure Factors (633 Kb) Retrieve 1Y6L in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1Y6L from S2C, [Save to disk] Re-refined 1y6l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1Y6L 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 1Y6L

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 1Y6L, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1y6la_, region A [Jmol] [rasmolscript] [script source]     - Domain d1y6lb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1y6lc_, region C [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1y6l_A] [1y6l_B] [1y6l_C] [1y6l] SWISS-PROT database: [Q96LR5] Domain organization of [UB2E2_HUMAN] by SWISSPFAM Domain found in 1Y6L: [UBCc ] by SMART

Other resources with information on 1Y6L

Community annotation for 1Y6L at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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