5YC1	Signaling Protein Peptide	date	Sep 06, 2017
title	Traf4_gpib Complex
authors	H.H.Park, C.M.Kim
compound		source
Molecule: Tnf Receptor-Associated Factor 4 Chain: A, B, C, D, E, F Fragment: Unp Residues 290-470 Synonym: Cysteine-Rich Domain Associated With Ring And Traf Protein 1,Metastatic Lymph Node Gene 62 Protein,Mln 62,Ring Protein 83; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Traf4, Cart1, Mln62, Rnf83 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Gpib Peptide Chain: G, I, K Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_taxid: 9606
symmetry	Space Group: P 1 21 1	R_factor 0.211 R_Free 0.265
crystal cell	length a length b length c angle alpha angle beta angle gamma 56.716 88.594 120.757 90.00 93.62 90.00
method	X-Ray Diffraction	resolution	2.51 Å
Gene Ontology	Chain Function Process Component F, A, D, C, E, B
Primary reference	Molecular basis for unique specificity of human TRAF4 for platelets GPIbbeta and GPVI., Kim CM, Son YJ, Kim S, Kim SY, Park HH, Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11422-11427. doi:, 10.1073/pnas.1708688114. Epub 2017 Oct 10. PMID:29073066

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (164 Kb) [Save to disk] Biological Unit Coordinates (5yc1.pdb1.gz) 80 Kb Biological Unit Coordinates (5yc1.pdb2.gz) 82 Kb CSU: Contacts of Structural Units for 5YC1 Structure Factors (821 Kb) Retrieve 5YC1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5YC1 from S2C, [Save to disk]

View 5YC1 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 5YC1

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 Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1m5yc1, region C:25-163,C:396-427 [Jmol] [rasmolscript] [script source]     - Domain d1d5yc1, region C:3-56 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5yc1_F] [5yc1_G] [5yc1_E] [5yc1_D] [5yc1_I] [5yc1_K] [5yc1_A] [5yc1_C] [5yc1_B] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5YC1

Community annotation for 5YC1 at PDBWiki (http://pdbwiki.org)

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