3IKR	Sugar Binding Protein	date	Aug 06, 2009
title	Crystal Structure Of Alpha 1-4 Mannobiose Bound Trimeric Hum Surfactant Protein D
authors	A.K.Shrive, T.J.Greenhough
compound		source
Molecule: Pulmonary Surfactant-Associated Protein D Chain: A, B, C Fragment: Unp Residues 199-375 Synonym: Sp-D, Psp-D, Lung Surfactant Protein D Engineered: Yes Mutation: Yes Other_details: Trimeric Fragment Comprising Alpha Helical N And Carbohydrate Recognition Domains		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Sftpd, Pspd, Sftp4 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid
symmetry	Space Group: P 1 21 1	R_factor 0.193 R_Free 0.212
crystal cell	length a length b length c angle alpha angle beta angle gamma 55.520 108.450 55.820 90.00 91.25 90.00
method	X-Ray Diffraction	resolution	1.65 Å
ligand	CA, MAN	enzyme
Primary reference	Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325., Shrive AK, Martin C, Burns I, Paterson JM, Martin JD, Townsend JP, Waters P, Clark HW, Kishore U, Reid KB, Greenhough TJ, J Mol Biol. 2009 Dec 11;394(4):776-88. Epub 2009 Sep 30. PMID:19799916

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk] Biological Unit Coordinates (3ikr.pdb1.gz) 80 Kb LPC: Ligand-Protein Contacts for 3IKR CSU: Contacts of Structural Units for 3IKR Structure Factors (3597 Kb) Retrieve 3IKR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3IKR from S2C, [Save to disk] Re-refined 3ikr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3IKR 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 3IKR

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 3IKR, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ikr_B] [3ikr_A] [3ikr] [3ikr_C] SWISS-PROT database: [P35247] Domain organization of [SFTPD_HUMAN] by SWISSPFAM Domain found in 3IKR: [CLECT ] by SMART

Other resources with information on 3IKR

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

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