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
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 Diffractionresolution 2.75 Å
ligand IO3 enzyme
A, B

Primary referenceCrystallographic 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.
  • 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] [2ydf_A] [2ydf_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YDF: [ALBUMIN ] by SMART
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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