3NV4	Sugar Binding Protein	date	Jul 07, 2010
title	Crystal Structure Of Human Galectin-9 C-Terminal Crd In Comp Sialyllactose
authors	H.Yoshida, S.Kamitori
compound		source
Molecule: Galectin 9 Short Isoform Variant Chain: A Fragment: C-Terminal Carbohydrate Recognition Domain, Resid 323; Synonym: Galectin-9 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-4t-2
symmetry	Space Group: P 63	R_factor 0.183 R_Free 0.226
crystal cell	length a length b length c angle alpha angle beta angle gamma 70.766 70.766 50.480 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.99 Å
ligand	BGC, GAL, NI, SIA	enzyme
Primary reference	X-ray Structures of Human Galectin-9 C-terminal Domain in Complexes with a Biantennary Oligosaccharide and Sialyllactose., Yoshida H, Teraoka M, Nishi N, Nakakita S, Nakamura T, Hirashima M, Kamitori S, J Biol Chem. 2010 Nov 19;285(47):36969-76. Epub 2010 Sep 22. PMID:20861009

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk] Biological Unit Coordinates (3nv4.pdb1.gz) 27 Kb LPC: Ligand-Protein Contacts for 3NV4 CSU: Contacts of Structural Units for 3NV4 Structure Factors (76 Kb) Retrieve 3NV4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3NV4 from S2C, [Save to disk] Re-refined 3nv4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3NV4 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3NV4

Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3NV4, from MSDmotif at EBI Fold representative 3nv4 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3nv4_A] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3NV4 with the sequences similar proteins can be viewed for 3NV4's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3NV4

Community annotation for 3NV4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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