3WHD	Immune System	date	Aug 24, 2013
title	C-Type Lectin, Human Mcl
authors	A.Furukawa, J.Kamishikiryo, D.Mori, K.Toyonaga, Y.Okabe, A.Toji, R Y.Miyake, T.Ose, S.Yamasaki, K.Maenaka
compound		source
Molecule: C-Type Lectin Domain Family 4 Member D Chain: A, C Fragment: Extracellular Domain, Unp Residues 61-215 Synonym: C-Type Lectin Superfamily Member 8, C-Type Lectin- Receptor 6, Clec-6; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Clec4d Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet22b
symmetry	Space Group: I 2 2 2	R_factor 0.176 R_Free 0.218
crystal cell	length a length b length c angle alpha angle beta angle gamma 85.190 96.056 104.826 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.29 Å
ligand	CA	enzyme
Primary reference	Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL., Furukawa A, Kamishikiryo J, Mori D, Toyonaga K, Okabe Y, Toji A, Kanda R, Miyake Y, Ose T, Yamasaki S, Maenaka K, Proc Natl Acad Sci U S A. 2013 Oct 7. PMID:24101491

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk] Biological Unit Coordinates (3whd.pdb1.gz) 28 Kb Biological Unit Coordinates (3whd.pdb2.gz) 28 Kb Biological Unit Coordinates (3whd.pdb3.gz) 55 Kb LPC: Ligand-Protein Contacts for 3WHD CSU: Contacts of Structural Units for 3WHD Structure Factors (298 Kb) Retrieve 3WHD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3WHD from S2C, [Save to disk] Re-refined 3whd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3WHD 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 3WHD

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 3WHD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3whd_A] [3whd] [3whd_C] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3WHD: [CLECT ] by SMART

Other resources with information on 3WHD

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

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