3ZNI	Ligase	date	Feb 14, 2013
title	Structure Of Phosphotyr363-Cbl-B - Ubch5b-Ub - Zap-70 Peptid
authors	H.Dou, L.Buetow, G.J.Sibbet, K.Cameron, D.T.Huang
compound		source
Molecule: E3 Ubiquitin-Protein Ligase Cbl-B Chain: A, E, I, M Fragment: Residues 36-427 Synonym: Casitas B-Lineage Lymphoma Proto-Oncogene B, Ring Protein 56, Sh3-Binding Protein Cbl-B, Signal Transduction Cbl-B; Ec: 6.3.2.19 Engineered: Yes Mutation: Yes Other_details: Y363 Is Phosphorylated. Gs At The N-Terminus Protein Resulted From Cloning.;		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)
Molecule: Tyrosine-Protein Kinase Zap-70 Chain: B, F, J, N Fragment: Residues 286-297 Synonym: 70 Kda Zeta-Chain Associated Protein, Syk-Related Kinase; Ec: 2.7.10.2 Engineered: Yes Other_details: Y292 Is Phosphorylated. In The Structure Y29 Numbered As 7.;		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Ubiquitin-Conjugating Enzyme E2 D2 Chain: C, G, K, O Fragment: Residues 2-147 Synonym: Ubiquitin Carrier Protein D2, Ubiquitin-Conjugatin E2(17)Kb 2, Ubiquitin-Conjugating Enzyme E2-17 Kda 2, Ubiqu Protein Ligase D2, Ubch5b, P53-Regulated Ubiquitin-Conjugat 1; Ec: 6.3.2.19 Engineered: Yes Mutation: Yes Other_details: K85 Sidechain In Chians C, G, K And O Forms Isopeptide Linkage With The Carbonyl Carbon Of G76 In Chain And P, Respectively.;		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)
Molecule: Polyubiquitin-C Chain: D, H, L, P Fragment: Residues 77-152 Synonym: Ubiquitin Engineered: Yes Other_details: Carbonyl Carbon Of G76 In Chians D, H, L And An Isopeptide Linkage With The Sidechain Of K85 In Chains C O, Respectively. Gsggs Linker At The N- Terminus Of Protein From Cloning		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 1 21 1	R_factor 0.175 R_Free 0.211
crystal cell	length a length b length c angle alpha angle beta angle gamma 94.970 131.800 122.000 90.00 91.92 90.00
method	X-Ray Diffraction	resolution	2.21 Å
ligand	CA, EDO, PTR, ZN	enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A, M, I, E O, C, K, G
Primary reference	Essentiality of a non-RING element in priming donor ubiquitin for catalysis by a monomeric E3., Dou H, Buetow L, Sibbet GJ, Cameron K, Huang DT, Nat Struct Mol Biol. 2013 Jul 14. doi: 10.1038/nsmb.2621. PMID:23851457

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (850 Kb) [Save to disk] Biological Unit Coordinates (3zni.pdb1.gz) 211 Kb Biological Unit Coordinates (3zni.pdb2.gz) 213 Kb Biological Unit Coordinates (3zni.pdb3.gz) 210 Kb Biological Unit Coordinates (3zni.pdb4.gz) 213 Kb LPC: Ligand-Protein Contacts for 3ZNI CSU: Contacts of Structural Units for 3ZNI Structure Factors (5227 Kb) Retrieve 3ZNI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3ZNI from S2C, [Save to disk] Re-refined 3zni structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3ZNI 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 3ZNI

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 3ZNI, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3zni_P] [3zni_L] [3zni_C] [3zni_H] [3zni_B] [3zni_O] [3zni_F] [3zni_J] [3zni_G] [3zni_A] [3zni_N] [3zni_D] [3zni_E] [3zni] [3zni_I] [3zni_M] [3zni_K] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3ZNI: [RING] [SH2] [UBCc] [UBQ ] by SMART

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Community annotation for 3ZNI at PDBWiki (http://pdbwiki.org)

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