2D39	Immune System	date	Sep 26, 2005
title	Trivalent Recognition Unit Of Innate Immunity System; Crystal Structure Of Human M-Ficolin Fibrinogen-Like Domain
authors	M.Tanio, S.Kondo, S.Sugio, T.Kohno
compound		source
Molecule: Ficolin-1 Chain: A, B, C Fragment: Fibrinogen Like Domain Synonym: Collagenfibrinogen Domain-Containing Protein 1, Ficolin-A, Ficolin A, M-Ficolin; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Pichia Pastoris Expression_system_taxid: 4922 Expression_system_strain: X-33 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ppiczalpha
symmetry	Space Group: P 1 21 1	R_factor 0.209 R_Free 0.240
crystal cell	length a length b length c angle alpha angle beta angle gamma 55.160 117.450 55.190 90.00 99.88 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	CA	enzyme
note	2D39 is a representative structure
Primary reference	Trivalent Recognition Unit of Innate Immunity System: CRYSTAL STRUCTURE OF TRIMERIC HUMAN M-FICOLIN FIBRINOGEN-LIKE DOMAIN., Tanio M, Kondo S, Sugio S, Kohno T, J Biol Chem. 2007 Feb 9;282(6):3889-95. Epub 2006 Dec 4. PMID:17148457

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk] Biological Unit Coordinates (2d39.pdb1.gz) 105 Kb LPC: Ligand-Protein Contacts for 2D39 CSU: Contacts of Structural Units for 2D39 Likely Quarternary Molecular Structure file(s) for 2D39 Structure Factors (437 Kb) Retrieve 2D39 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2D39 from S2C, [Save to disk] Re-refined 2d39 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2D39 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 2D39

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 2D39, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2d39_B] [2d39_A] [2d39] [2d39_C] SWISS-PROT database: [O00602] Domain organization of [FCN1_HUMAN] by SWISSPFAM Domain found in 2D39: [FBG ] by SMART

Other resources with information on 2D39

Community annotation for 2D39 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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