3DBZ	Sugar Binding Protein	date	Jun 02, 2008
title	Human Surfactant Protein D
authors	J.F.Head
compound		source
Molecule: Pulmonary Surfactant-Associated Protein D Chain: A, B, C Fragment: Head And Neck Domain, Unp Residues 223-375 Synonym: Sp-D, Psp-D, Lung Surfactant Protein D Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Man Organism_taxid: 9606 Gene: Sftpd, Pspd, Sftp4 Expression_system: Escherichia Coli Expression_system_strain: Rosettablue Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30a(+)
symmetry	Space Group: P 1 21 1	R_factor 0.180 R_Free 0.202
crystal cell	length a length b length c angle alpha angle beta angle gamma 55.260 107.600 55.600 90.00 91.80 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	CA, MPD	enzyme
Primary reference	Interaction of recombinant surfactant protein D with lipopolysaccharide: conformation and orientation of bound protein by IRRAS and simulations., Wang L, Brauner JW, Mao G, Crouch E, Seaton B, Head J, Smith K, Flach CR, Mendelsohn R, Biochemistry. 2008 Aug 5;47(31):8103-13. Epub 2008 Jul 12. PMID:18620419

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk] Biological Unit Coordinates (3dbz.pdb1.gz) 81 Kb LPC: Ligand-Protein Contacts for 3DBZ CSU: Contacts of Structural Units for 3DBZ Likely Quarternary Molecular Structure file(s) for 3DBZ Structure Factors (741 Kb) Retrieve 3DBZ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DBZ from S2C, [Save to disk] Re-refined 3dbz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DBZ 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 3DBZ

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 3DBZ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dbz_C] [3dbz] [3dbz_B] [3dbz_A] SWISS-PROT database: [P35247] Domain organization of [SFTPD_HUMAN] by SWISSPFAM Domain found in 3DBZ: [CLECT ] by SMART

Other resources with information on 3DBZ

Community annotation for 3DBZ at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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