2YDF	Transport Protein	date	Mar 18, 2011
title	Human Serum Albumin Complexed With Iophenoxic Acid
authors	A.J.Ryan, S.Curry
compound		source
Molecule: Serum Albumin Chain: A, B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Serum Expression_system: Pichia Pastoris Expression_system_taxid: 4922
symmetry	Space Group: P 1	R_factor 0.2066 R_Free 0.2393
crystal cell	length a length b length c angle alpha angle beta angle gamma 55.072 55.440 119.845 81.00 90.83 64.52
method	X-Ray Diffraction	resolution	2.75 Å
ligand	IO3	enzyme
Gene Ontology	Chain Function Process Component A, B DNA binding fatty acid binding copper ion binding protein binding drug binding zinc ion binding lipid binding toxic substance binding antioxidant activity oxygen binding enzyme binding pyridoxal phosphate binding cell surface binding metal ion binding chaperone binding platelet degranulation lipid metabolic process transport response to stress response to nutrient blood coagulation bile acid metabolic process cellular response to starvat... response to organic substanc... bile acid and bile salt tran... hemolysis by symbiont of hos... platelet activation lipoprotein metabolic proces... negative regulation of apopt... negative regulation of progr... sodium-independent organic a... small molecule metabolic pro... positive regulation of circa... response to mercury ion maintenance of mitochondrion... transmembrane transport response to platinum ion extracellular region basement membrane extracellular space cytoplasm platelet alpha granule lumen... protein complex extracellular vesicular exos...
Primary reference	Crystallographic analysis reveals the structural basis of the high-affinity binding of Iophenoxic acid to Human Serum Albumin., Ryan AJ, Chung CW, Curry S, BMC Struct Biol. 2011 Apr 18;11(1):18. PMID:21501503

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (335 Kb) [Save to disk] Biological Unit Coordinates (2ydf.pdb1.gz) 161 Kb Biological Unit Coordinates (2ydf.pdb2.gz) 164 Kb LPC: Ligand-Protein Contacts for 2YDF CSU: Contacts of Structural Units for 2YDF Structure Factors (277 Kb) Retrieve 2YDF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2YDF from S2C, [Save to disk] Re-refined 2ydf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2YDF 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 2YDF

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 2YDF, from MSDmotif at EBI Fold representative 2ydf from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ydf_A] [2ydf_B] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 2YDF with the sequences similar proteins can be viewed for 2YDF'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 2YDF

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

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