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 Diffractionresolution 2.52 Å
ligand DKA, NPS enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural 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.
  • 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_B] [2vdb_A] [2vdb]
  • SWISS-PROT database: [P02768] [Q51911]
  • Domain organization of [ALBU_HUMAN] [PAB_PEPMA] by SWISSPFAM
  • Domain found in 2VDB: [ALBUMIN ] by SMART
  • Other resources with information on 2VDB
  • Community annotation for 2VDB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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