2VDB	Protein Binding	date	Oct 04, 2007
title	Structure Of Human Serum Albumin With S-Naproxen And The Ga Module
authors	S.Lejon, J.F.Cramer, P.A.Nordberg
compound		source
Molecule: Serum Albumin Chain: A Fragment: Residues 30-608 Synonym: Human Serum Albumin		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Serum
Molecule: Peptostreptococcal Albumin-Binding Protein Chain: B Fragment: Residues 213-265 Synonym: Ga Module Engineered: Yes		Organism_scientific: Peptostreptococcus Magnus Organism_taxid: 1260 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_plasmid: Pet28
symmetry	Space Group: C 1 2 1	R_factor 0.234 R_Free 0.280
crystal cell	length a length b length c angle alpha angle beta angle gamma 190.507 49.462 79.933 90.00 93.00 90.00
method	X-Ray Diffraction	resolution	2.52 Å
ligand	DKA, NPS	enzyme
Gene Ontology	Chain Function Process Component A 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	Structural basis for the binding of naproxen to human serum albumin in the presence of fatty acids and the GA module., Lejon S, Cramer JF, Nordberg P, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Feb 1;64(Pt, 2):64-9. Epub 2008 Jan 18. PMID:18259051

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk] Biological Unit Coordinates (2vdb.pdb1.gz) 98 Kb LPC: Ligand-Protein Contacts for 2VDB CSU: Contacts of Structural Units for 2VDB Likely Quarternary Molecular Structure file(s) for 2VDB Structure Factors (339 Kb) Retrieve 2VDB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VDB from S2C, [Save to disk] Re-refined 2vdb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VDB 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 2VDB

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vdb_A] [2vdb_B] SWISS-PROT database: [P02768] [Q51911] Domain organization of [ALBU_HUMAN] [PAB_PEPMA] by SWISSPFAM Domain found in 2VDB: [ALBUMIN ] by SMART Alignments of the sequence of 2VDB with the sequences similar proteins can be viewed for 2VDB's classification [ALBU_HUMAN] [PAB_PEPMA] 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 [ALBU_HUMAN] [PAB_PEPMA] at ProtoMap. Click on the Cluster number.

Other resources with information on 2VDB

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

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